Updating workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b from 0.7.1 to 0.7.2 #511

gxydevbot · 2024-08-19T04:24:23Z

Hello! This is an automated update of the following workflow: workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b. I created this PR because I think one or more of the component tools are out of date, i.e. there is a newer version available on the ToolShed.

By comparing with the latest versions available on the ToolShed, it seems the following tools are outdated:

toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy1 should be updated to toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2

The workflow release number has been updated from 0.7.1 to 0.7.2.

gxydevbot · 2024-08-26T04:22:22Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-02T04:22:21Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-09T04:23:51Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-16T04:22:51Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-23T04:24:07Z

There are new updates, if you want to integrate them, close the PR and delete branch.

gxydevbot · 2024-09-23T14:02:22Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-09-23T15:06:22Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Purging-duplicates-one-haplotype-VGP6b.ga_0

Problems:

Output with path /tmp/tmpyn08_w1f/Busco on data 36 short summary__3ad00b48-14a5-481b-84f9-caf05916b964 different than expected
Expected text 'C:1.1%[S:1.1%,D:0.0%],F:0.5%,M:98.4%,n:3354' in output ('# BUSCO version is: 5.7.1 
# The lineage dataset is: vertebrata_odb10 (Creation date: 2021-02-19, number of genomes: 67, number of BUSCOs: 3354)
# Summarized benchmarking in BUSCO notation for file /tmp/tmpp3xor7px/files/0/d/8/dataset_0d8cea20-4d0c-4279-a401-cf72b1e09ef1.dat
# BUSCO was run in mode: euk_genome_min
# Gene predictor used: miniprot

	***** Results: *****

	C:1.0%[S:1.0%,D:0.0%],F:0.1%,M:98.9%,n:3354,E:2.9%	   
	35	Complete BUSCOs (C)	(of which 1 contain internal stop codons)		   
	34	Complete and single-copy BUSCOs (S)	   
	1	Complete and duplicated BUSCOs (D)	   
	4	Fragmented BUSCOs (F)			   
	3315	Missing BUSCOs (M)			   
	3354	Total BUSCO groups searched		   

Assembly Statistics:
	79	Number of scaffolds
	79	Number of contigs
	1884297	Total length
	0.000%	Percent gaps
	21 KB	Scaffold N50
	21 KB	Contigs N50


Dependencies and versions:
	hmmsearch: 3.1
	bbtools: None
	miniprot_index: 0.13-r248
	miniprot_align: 0.13-r248
	python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0)
	busco: 5.7.1
')

Workflow invocation details

Invocation Messages

Steps

Step 1: Genomescope model parameters:
- step_state: scheduled
Step 2: Pacbio Reads Collection - Trimmed:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types float,float,float,float,float,int  --file '/tmp/tmpp3xor7px/job_working_directory/000/7/configs/tmphqj_2i2l' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpp3xor7px/files/7/a/e/dataset_7aeb07a5-4bc3-452a-a3cf-4148d85e32a4.dat' '/tmp/tmpp3xor7px/job_working_directory/000/7/outputs/dataset_2a0b26f1-5151-4bbc-9f85-4f91dcbe1c2f.dat'

Exit Code:

```
0
```

Standard Output:

1.5*c3
3*c7
Computing 2 new columns with instructions ['1.5*c3;;', '3*c7;;']
Computed new column values for 100.00% of 1 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "1.5c3"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "3c7"}], "header_lines_select": "no"}`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpp3xor7px/files/b/6/8/dataset_b681ff2f-d0fa-4092-8c34-ae894b1a75f6.dat' reference.fa && minimap2 -x asm5    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmpp3xor7px/files/b/5/f/dataset_b5fb5b86-df86-4185-88d8-9bdf2cc69ff3.dat' > '/tmp/tmpp3xor7px/job_working_directory/000/8/outputs/dataset_0ce07597-06c5-4da4-95ca-ef36d8e4a382.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.068*0.92] collected minimizers
[M::mm_idx_gen::0.087*0.92] sorted minimizers
[M::main::0.087*0.92] loaded/built the index for 86 target sequence(s)
[M::mm_mapopt_update::0.089*0.92] mid_occ = 54
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 86
[M::mm_idx_stat::0.091*0.92] distinct minimizers: 156208 (93.94% are singletons); average occurrences: 1.302; average spacing: 9.990; total length: 2031175
[M::worker_pipeline::60.733*0.99] mapped 5789 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -x asm5 --q-occ-frac 0.01 -t 1 reference.fa /tmp/tmpp3xor7px/files/b/5/f/dataset_b5fb5b86-df86-4185-88d8-9bdf2cc69ff3.dat
[M::main] Real time: 60.736 sec; CPU: 60.077 sec; Peak RSS: 0.071 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
alignment_options	`{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "asm5", "fastq_input1": {"values": [{"id": 1, "src": "dce"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "paf"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 2, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

split_fa '/tmp/tmpp3xor7px/files/b/6/8/dataset_b681ff2f-d0fa-4092-8c34-ae894b1a75f6.dat' > split.fasta

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 1, "functions": "split_fa", "input": {"values": [{"id": 2, "src": "hda"}]}}`

Step 14: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpp3xor7px/files/9/1/1/dataset_911248f3-ad92-44a1-b8f5-8941e9a38dbd.dat' --out-size c   --tabular > '/tmp/tmpp3xor7px/job_working_directory/000/10/outputs/dataset_9615ddfd-a061-4d94-8d6f-a2e6c6bf1186.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 15: Estimated genome size:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 16: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpp3xor7px/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpp3xor7px/files/2/a/0/dataset_2a0b26f1-5151-4bbc-9f85-4f91dcbe1c2f.dat' 'c8' T '/tmp/tmpp3xor7px/job_working_directory/000/12/outputs/dataset_cc114360-0151-4bf2-be3d-47e57730b56d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8"`
dbkey	`"?"`
delimiter	`"T"`

Step 17: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpp3xor7px/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpp3xor7px/files/2/a/0/dataset_2a0b26f1-5151-4bbc-9f85-4f91dcbe1c2f.dat' 'c7' T '/tmp/tmpp3xor7px/job_working_directory/000/13/outputs/dataset_cdcc884f-a7a4-44b7-b7df-b02762665b5b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 18: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpp3xor7px/files/d/a/e/dataset_dae7e3ef-539f-48b3-99be-49ba8c511cec.dat' reference.fa && minimap2 -DP -k19 -w19 -m200    --min-occ-floor 100 --q-occ-frac 0.01 -m 40  -A 1 -B 19 -O 39,81 -E 3,1 -z 200      -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmpp3xor7px/files/d/a/e/dataset_dae7e3ef-539f-48b3-99be-49ba8c511cec.dat' > '/tmp/tmpp3xor7px/job_working_directory/000/14/outputs/dataset_11df2421-98e9-45fa-87d2-86c21a744e86.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.057*1.02] collected minimizers
[M::mm_idx_gen::0.076*1.01] sorted minimizers
[M::main::0.076*1.01] loaded/built the index for 86 target sequence(s)
[M::mm_mapopt_update::0.079*1.01] mid_occ = 100
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 86
[M::mm_idx_stat::0.081*1.01] distinct minimizers: 156208 (93.94% are singletons); average occurrences: 1.302; average spacing: 9.990; total length: 2031175
[M::worker_pipeline::1.534*0.91] mapped 86 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -DP -k19 -w19 -m200 --min-occ-floor 100 --q-occ-frac 0.01 -m 40 -A 1 -B 19 -O 39,81 -E 3,1 -z 200 -t 1 reference.fa /tmp/tmpp3xor7px/files/d/a/e/dataset_dae7e3ef-539f-48b3-99be-49ba8c511cec.dat
[M::main] Real time: 1.540 sec; CPU: 1.399 sec; Peak RSS: 0.028 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
alignment_options	`{"A": "1", "B": "19", "E": "3", "E2": "1", "O": "39", "O2": "81", "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": "200", "z2": null}`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "self-homology", "fastq_input1": {"values": [{"id": 9, "src": "hda"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "paf"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": "40", "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": "100", "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 19: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpp3xor7px/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmpp3xor7px/files/9/6/1/dataset_9615ddfd-a061-4d94-8d6f-a2e6c6bf1186.dat' --output='/tmp/tmpp3xor7px/job_working_directory/000/15/outputs/dataset_3768277f-695e-4bcb-b663-90426ecd565c.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"93678c3779b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpp3xor7px/job_working_directory/000/16/configs/tmpmg5xvt3c' '/tmp/tmpp3xor7px/files/3/7/6/dataset_3768277f-695e-4bcb-b663-90426ecd565c.dat' > '/tmp/tmpp3xor7px/job_working_directory/000/16/outputs/dataset_4d83aa27-1159-4087-8497-6a60c0ec0e4a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3779b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmpp3xor7px/files/4/d/8/dataset_4d83aa27-1159-4087-8497-6a60c0ec0e4a.dat > '/tmp/tmpp3xor7px/job_working_directory/000/17/outputs/dataset_9960fc85-789e-42a7-a4dc-6e2fca6945f0.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3779b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpp3xor7px/files/4/d/8/dataset_4d83aa27-1159-4087-8497-6a60c0ec0e4a.dat" "/tmp/tmpp3xor7px/job_working_directory/000/18/outputs/dataset_fe1ccd62-c542-433a-a76c-f738c4cdb493.dat" "1" "yes"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3779b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"93678c3779b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3779b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1933626", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmpp3xor7px/job_working_directory/000/43/configs/tmpsa3i_pi1' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpp3xor7px/files/f/e/1/dataset_fe1ccd62-c542-433a-a76c-f738c4cdb493.dat' '/tmp/tmpp3xor7px/job_working_directory/000/43/outputs/dataset_d2a970bf-e977-4737-943e-ffe43d6799a4.dat'

Exit Code:

```
0
```

Standard Output:

c3/1933626
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1933626;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 79 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3779b911efaec4d19c379fcbf3"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1933626"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 20: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpp3xor7px/files/9/1/1/dataset_911248f3-ad92-44a1-b8f5-8941e9a38dbd.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmpp3xor7px/job_working_directory/000/22/outputs/dataset_e7f0b9ba-bf6a-41db-b2f1-51cd64b5425d.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 3: Assembly to purge:
- step_state: scheduled

Step 21: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 22: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpp3xor7px/job_working_directory/000/23/configs/tmpb13v_3bs' '/tmp/tmpp3xor7px/files/e/7/f/dataset_e7f0b9ba-bf6a-41db-b2f1-51cd64b5425d.dat' > '/tmp/tmpp3xor7px/job_working_directory/000/23/outputs/dataset_4cd62e08-190a-445b-a287-280ee757c025.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN{print \"Metric\\tAlternate\"}; {print}; "`
dbkey	`"?"`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gzip -c '/tmp/tmpp3xor7px/files/0/c/e/dataset_0ce07597-06c5-4da4-95ca-ef36d8e4a382.dat' > '0.gz' && pbcstat -M 500 -f 0.0 -l 0 -p '0.gz' && mv PB.stat depth.stat && calcuts -f 0.1 -l 1 -m 16 -u 48 -d 0 depth.stat > cutoffs.tsv 2>calcuts.log && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/e9bd16ba5ebd/purge_dups/hist_plot.py' --cutoffs cutoffs.tsv --title 'Read depth histogram plot' depth.stat hist.png

Exit Code:

```
0
```

Standard Error:

Program starts
Program finished successfully

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	{"__current_case__": 2, "functions": "pbcstat", "input": {"values": [{"id": 2, "src": "hdca"}]}, "output_options": ["pbcstat_coverage", "pbcstat_wig", "depth_stats", "histogram", "calcuts_cutoff", "calcuts_log"], "pbcstat_options": {"flank": "0", "max_cov": "500", "min_map_qual": null, "min_map_ratio": "0.0", "primary_alignments": true}, "section_calcuts": {"low_depth": "1", "min_depth": "0.1", "ploidy": "-d 0", "transition": "16", "upper_depth": "48"}, "section_hist": {"title": "Read depth histogram plot", "xmax": null, "xmin": null, "ymax": null, "ymin": null}}

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gzip -c '/tmp/tmpp3xor7px/files/1/1/d/dataset_11df2421-98e9-45fa-87d2-86c21a744e86.dat' > '0.gz' && purge_dups -c '/tmp/tmpp3xor7px/files/6/a/1/dataset_6a12c8a2-07a9-448d-aa1d-f460c68d65d3.dat' -T '/tmp/tmpp3xor7px/files/8/2/a/dataset_82a3220e-d7d3-4c7c-acf2-a23ef1e131f2.dat' -f 0.8 -a 70 -b 200 -m 500 -M 20000 -l 10000 -E 15000 '0.gz' > dups.bed 2> purge_dups.log

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 0, "coverage": {"values": [{"id": 25, "src": "hda"}]}, "cutoffs": {"values": [{"id": 29, "src": "hda"}]}, "double_chain": {"__current_case__": 1, "chaining_rounds": "one"}, "functions": "purge_dups", "input": {"values": [{"id": 14, "src": "hda"}]}, "log_file": true, "max_extend": "15000", "max_gap": "20000", "min_align": "70", "min_bad": "0.8", "min_chain": "500", "min_chain_score": "10000", "min_match": "200"}`

Step 26: Remove REPEATs from BED:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

grep -P -A 0 -B 0 --no-group-separator -v -i -- 'REPEAT' '/tmp/tmpp3xor7px/files/3/8/d/dataset_38da6a5e-2d36-4c57-a44b-d81daba07445.dat' > '/tmp/tmpp3xor7px/job_working_directory/000/26/outputs/dataset_15c9fe91-96cc-415d-85fb-b124a235e8bd.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`"-v"`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-P"`
url_paste	`"REPEAT"`

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

get_seqs   -e  -l 10000 -m 0.05 -g 10000 '/tmp/tmpp3xor7px/files/1/5/c/dataset_15c9fe91-96cc-415d-85fb-b124a235e8bd.dat' '/tmp/tmpp3xor7px/files/b/6/8/dataset_b681ff2f-d0fa-4092-8c34-ae894b1a75f6.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 5, "advanced_options": {"coverage": false, "end_trim": true, "haplotigs": false, "length": "10000", "min_gap": "10000", "min_ratio": "0.05", "split": false}, "bed_input": {"values": [{"id": 32, "src": "hda"}]}, "fasta_input": {"values": [{"id": 2, "src": "hda"}]}, "functions": "get_seqs"}`

Step 28: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p output_files && mkdir -p read-db.meryl && tar -zxf /tmp/tmpp3xor7px/files/d/3/b/dataset_d3b40f50-d831-4f84-9a3f-f6ba6a9e5cae.dat -C read-db.meryl --strip-components=1 && ln -s '/tmp/tmpp3xor7px/files/0/d/8/dataset_0d8cea20-4d0c-4279-a401-cf72b1e09ef1.dat' assembly_01.fasta && ln -s '/tmp/tmpp3xor7px/files/9/1/1/dataset_911248f3-ad92-44a1-b8f5-8941e9a38dbd.dat' assembly_02.fasta && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta output_merqury &> /tmp/tmpp3xor7px/job_working_directory/000/28/outputs/dataset_3cb1f02e-a1f1-4cbb-9ecc-e3a873139c85.dat && mv output_merqury* output_files && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
label	`"output_merqury"`
mode	`{"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 34, "src": "hda"}]}, "assembly_02": {"values": [{"id": 5, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 3, "src": "hda"}]}, "options": "default"}`
output_add_headers	`false`
output_selector	`["qv", "plots", "stats", "log", "hist"]`

Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpp3xor7px/files/0/d/8/dataset_0d8cea20-4d0c-4279-a401-cf72b1e09ef1.dat' --out-size c   --tabular > '/tmp/tmpp3xor7px/job_working_directory/000/29/outputs/dataset_fa12c7f3-257b-4315-82c3-c0e73cd113b2.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 30: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmpp3xor7px/files/0/d/8/dataset_0d8cea20-4d0c-4279-a401-cf72b1e09ef1.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'vertebrata_odb10'  --miniprot  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-09-23 15:00:05 ERROR:	Something went wrong. Results not recorded.
2024-09-23 15:00:05 ERROR:	BUSCO analysis failed!
2024-09-23 15:00:05 ERROR:	Check the logs, read the user guide (https://busco.ezlab.org/busco_userguide.html), and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues

Standard Output:

2024-09-23 14:42:48 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 09/23/2024 14:42:48 *****
2024-09-23 14:42:48 INFO:	Configuring BUSCO with local environment
2024-09-23 14:42:48 INFO:	Running genome mode
2024-09-23 14:42:51 INFO:	Input file is /tmp/tmpp3xor7px/files/0/d/8/dataset_0d8cea20-4d0c-4279-a401-cf72b1e09ef1.dat
2024-09-23 14:42:51 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_min
2024-09-23 14:42:51 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_min
2024-09-23 14:42:51 INFO:	Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2021-02-19)
2024-09-23 14:42:51 INFO:	Running 1 job(s) on bbtools, starting at 09/23/2024 14:42:51
2024-09-23 14:42:53 INFO:	[bbtools]	1 of 1 task(s) completed
2024-09-23 14:42:53 INFO:	Running 1 job(s) on miniprot_index, starting at 09/23/2024 14:42:53
2024-09-23 14:42:53 INFO:	[miniprot_index]	1 of 1 task(s) completed
2024-09-23 14:42:53 INFO:	Running 1 job(s) on miniprot_align, starting at 09/23/2024 14:42:53
2024-09-23 14:59:08 INFO:	[miniprot_align]	1 of 1 task(s) completed
2024-09-23 14:59:14 INFO:	***** Run HMMER on gene sequences *****
2024-09-23 14:59:15 INFO:	Running 612 job(s) on hmmsearch, starting at 09/23/2024 14:59:15
2024-09-23 14:59:22 INFO:	[hmmsearch]	62 of 612 task(s) completed
2024-09-23 14:59:27 INFO:	[hmmsearch]	123 of 612 task(s) completed
2024-09-23 14:59:31 INFO:	[hmmsearch]	184 of 612 task(s) completed
2024-09-23 14:59:36 INFO:	[hmmsearch]	245 of 612 task(s) completed
2024-09-23 14:59:41 INFO:	[hmmsearch]	307 of 612 task(s) completed
2024-09-23 14:59:46 INFO:	[hmmsearch]	368 of 612 task(s) completed
2024-09-23 14:59:50 INFO:	[hmmsearch]	429 of 612 task(s) completed
2024-09-23 14:59:54 INFO:	[hmmsearch]	490 of 612 task(s) completed
2024-09-23 14:59:59 INFO:	[hmmsearch]	551 of 612 task(s) completed
2024-09-23 15:00:04 INFO:	[hmmsearch]	612 of 612 task(s) completed
2024-09-23 15:00:04 INFO:	45 exons in total
2024-09-23 15:00:04 WARNING:	1 of 35 Complete matches (2.9%) contain internal stop codons in Miniprot gene predictions
2024-09-23 15:00:04 WARNING:	BUSCO gene predictions from Miniprot have low average identity (0.4699999988079071). You may want to repeat the analysis using the Metaeuk pipeline.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "use_augustus_selector": "miniprot"}}`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "missing", "image", "gff"]`

Step 4: Meryl Database:
- step_state: scheduled

Step 31: Convert purged fasta to gfa:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpp3xor7px/files/0/d/8/dataset_0d8cea20-4d0c-4279-a401-cf72b1e09ef1.dat'  -o dataset.gfa --discover-terminal-overlaps 1000 --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 79
Total scaffold length: 1884297
Average scaffold length: 23851.86
Scaffold N50: 21449
Scaffold auN: 34441.92
Scaffold L50: 28
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 79
Total contig length: 1884297
Average contig length: 23851.86
Contig N50: 21449
Contig auN: 34441.92
Contig L50: 28
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 577767:363592:365584:577354
GC content %: 38.70
# soft-masked bases: 0
# segments: 79
Total segment length: 1884297
Average segment length: 23851.86
# gaps: 0
# paths: 79
# edges: 1
Average degree: 0.01
# connected components: 1
Largest connected component length: 71428
# dead ends: 156
# disconnected components: 77
Total length disconnected components: 1812869
# separated components: 78
# bubbles: 0
# circular segments: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 1, "terminal_overlaps_length": "1000", "terminal_overlaps_select": "yes"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 32: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpp3xor7px/files/0/d/8/dataset_0d8cea20-4d0c-4279-a401-cf72b1e09ef1.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmpp3xor7px/job_working_directory/000/32/outputs/dataset_817a81a6-7fba-4e86-b450-67a7ae0cd3b2.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 33: merqury_QV:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
input	`{"values": [{"id": 3, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury", "which_dataset": "by_identifier"}`

Step 34: output_merqury.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 35: output_merqury.spectra-asm.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.spectra-asm.fl", "which_dataset": "by_identifier"}`

Step 36: output_merqury.assembly_01.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.assembly_01.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 37: merqury_stats:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
input	`{"values": [{"id": 5, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 38: output_merqury.assembly_02.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.assembly_02.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 39: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpp3xor7px/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmpp3xor7px/files/f/a/1/dataset_fa12c7f3-257b-4315-82c3-c0e73cd113b2.dat' --output='/tmp/tmpp3xor7px/job_working_directory/000/33/outputs/dataset_0d398827-cafe-4575-8c4b-cbeaaac5e928.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"93678c3879b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpp3xor7px/job_working_directory/000/34/configs/tmpdgg5uw50' '/tmp/tmpp3xor7px/files/0/d/3/dataset_0d398827-cafe-4575-8c4b-cbeaaac5e928.dat' > '/tmp/tmpp3xor7px/job_working_directory/000/34/outputs/dataset_3f7026ba-2dbb-4175-ab68-aedbc3c623b9.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3879b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmpp3xor7px/files/3/f/7/dataset_3f7026ba-2dbb-4175-ab68-aedbc3c623b9.dat > '/tmp/tmpp3xor7px/job_working_directory/000/35/outputs/dataset_f54d717d-ccc8-4c74-87d4-8c6327a039c2.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3879b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpp3xor7px/files/3/f/7/dataset_3f7026ba-2dbb-4175-ab68-aedbc3c623b9.dat" "/tmp/tmpp3xor7px/job_working_directory/000/36/outputs/dataset_6380aca4-356e-40e0-86e2-ae69b231629d.dat" "1" "yes"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3879b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"93678c3879b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3879b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1884297", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmpp3xor7px/job_working_directory/000/45/configs/tmpyj2bxeqe' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpp3xor7px/files/6/3/8/dataset_6380aca4-356e-40e0-86e2-ae69b231629d.dat' '/tmp/tmpp3xor7px/job_working_directory/000/45/outputs/dataset_66537a03-d9b3-48c8-94f9-2701ae4f9d10.dat'

Exit Code:

```
0
```

Standard Output:

c3/1884297
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1884297;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 79 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3879b911efaec4d19c379fcbf3"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1884297"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 40: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpp3xor7px/job_working_directory/000/38/configs/tmpymbsgiv2' '/tmp/tmpp3xor7px/files/8/1/7/dataset_817a81a6-7fba-4e86-b450-67a7ae0cd3b2.dat' > '/tmp/tmpp3xor7px/job_working_directory/000/38/outputs/dataset_74f38653-0f8b-46b6-ba55-8f27688452f3.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN{print \"Metric\\tPrimary\"}; {print}; "`
dbkey	`"?"`

Step 5: Assembly to leave alone (For Merqury comparison):
- step_state: scheduled

Step 41: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Primary data:
- step_state: scheduled
Step 2: Alternate data:
- step_state: scheduled

Step 11: Size Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpp3xor7px/job_working_directory/000/52/configs/tmp3timtrr9' && Rscript '/tmp/tmpp3xor7px/job_working_directory/000/52/configs/tmp3timtrr9'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmpp3xor7px/files/d/8/4/dataset_d84bea3d-a7f3-4b54-9a65-c31a33b7ce0c.dat', sep='\t', header=TRUE)

names(input)[2] <- "xcol"
names(input)[3] <- "ycol"

    gg_facet = NULL
    gg_factor = aes(colour=factor(factor))

        gg_line = geom_line(size=1, alpha=1, gg_factor)

        color_scale = scale_color_brewer(palette='Set1', direction='1')

    names(input)[1] <- "factor"


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmpp3xor7px/job_working_directory/000/52/outputs/dataset_198631c5-9ca3-463f-bdcc-805cdb183c4e.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3979b911efaec4d19c379fcbf3"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"Scaffold number"`
xplot	`"2"`
ylab	`"Cumulative Size (Mb)"`
yplot	`"3"`

Step 3: Name of primary assembly:
- step_state: scheduled
Step 4: Name of alternate assembly:
- step_state: scheduled

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpp3xor7px/files/6/6/5/dataset_66537a03-d9b3-48c8-94f9-2701ae4f9d10.dat" "/tmp/tmpp3xor7px/job_working_directory/000/46/outputs/dataset_b5ffa8c7-e0f3-49d2-b080-389f0bf37fc5.dat" "Hap1" "no"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3979b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Hap1"`
iterate	`"no"`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpp3xor7px/files/d/2/a/dataset_d2a970bf-e977-4737-943e-ffe43d6799a4.dat" "/tmp/tmpp3xor7px/job_working_directory/000/47/outputs/dataset_828ff898-3314-41f3-ba2c-670af123e2c8.dat" "Hap2" "no"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3979b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Hap2"`
iterate	`"no"`

Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpp3xor7px/files/b/5/f/dataset_b5ffa8c7-e0f3-49d2-b080-389f0bf37fc5.dat' >> '/tmp/tmpp3xor7px/job_working_directory/000/48/outputs/dataset_d012ac27-d593-422a-bdfb-301d8326d4b1.dat' && cat '/tmp/tmpp3xor7px/files/8/2/8/dataset_828ff898-3314-41f3-ba2c-670af123e2c8.dat' >> '/tmp/tmpp3xor7px/job_working_directory/000/48/outputs/dataset_d012ac27-d593-422a-bdfb-301d8326d4b1.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3979b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "inputs2": {"values": [{"id": 58, "src": "hda"}]}}]`

Step 8: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpp3xor7px/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpp3xor7px/files/d/0/1/dataset_d012ac27-d593-422a-bdfb-301d8326d4b1.dat' 'c8,c5,c6' T '/tmp/tmpp3xor7px/job_working_directory/000/49/outputs/dataset_b7eecad6-2924-4ca7-aa87-875393065778.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"93678c3979b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8,c5,c6"`
dbkey	`"?"`
delimiter	`"T"`

Step 9: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpp3xor7px/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpp3xor7px/files/d/0/1/dataset_d012ac27-d593-422a-bdfb-301d8326d4b1.dat' 'c8,c4,c7' T '/tmp/tmpp3xor7px/job_working_directory/000/50/outputs/dataset_d84bea3d-a7f3-4b54-9a65-c31a33b7ce0c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"93678c3979b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8,c4,c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 10: Nx Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpp3xor7px/job_working_directory/000/51/configs/tmpwbdfg7qv' && Rscript '/tmp/tmpp3xor7px/job_working_directory/000/51/configs/tmpwbdfg7qv'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmpp3xor7px/files/b/7/e/dataset_b7eecad6-2924-4ca7-aa87-875393065778.dat', sep='\t', header=TRUE)

names(input)[2] <- "xcol"
names(input)[3] <- "ycol"

    gg_facet = NULL
    gg_factor = aes(colour=factor(factor))

        gg_line = geom_line(size=1, alpha=1, gg_factor)

        color_scale = scale_color_brewer(palette='Set1', direction='1')

    names(input)[1] <- "factor"


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmpp3xor7px/job_working_directory/000/51/outputs/dataset_086a9d62-2774-49f7-989b-5b8abc5557f0.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3979b911efaec4d19c379fcbf3"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"x"`
xplot	`"2"`
ylab	`"Nx (Mb)"`
yplot	`"3"`

Step 42: join1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpp3xor7px/galaxy-dev/tools/filters/join.py' '/tmp/tmpp3xor7px/files/7/4/f/dataset_74f38653-0f8b-46b6-ba55-8f27688452f3.dat' '/tmp/tmpp3xor7px/files/4/c/d/dataset_4cd62e08-190a-445b-a287-280ee757c025.dat' 1 1 '/tmp/tmpp3xor7px/job_working_directory/000/39/outputs/dataset_7db6ee5f-3231-4773-886b-ac1bfc98c33c.dat' -u -p --index_depth=3 --buffer=50000000 --fill_options_file=/tmp/tmpp3xor7px/job_working_directory/000/39/configs/tmp5z5euapf

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
field1	`"1"`
field2	`"1"`
fill_empty_columns	`{"__current_case__": 1, "do_fill_empty_columns": {"__current_case__": 0, "column_fill_type": "single_fill_value", "fill_value": "."}, "fill_columns_by": "fill_unjoined_only", "fill_empty_columns_switch": "fill_empty"}`
header	`""`
partial	`"-p"`
unmatched	`"-u"`

Step 43: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cut --complement -f '3' '/tmp/tmpp3xor7px/files/7/d/b/dataset_7db6ee5f-3231-4773-886b-ac1bfc98c33c.dat' > '/tmp/tmpp3xor7px/job_working_directory/000/40/outputs/dataset_6038b8a1-888c-4aa5-a951-a9458e306ef8.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
complement	`"--complement"`
cut_type_options	`{"__current_case__": 0, "colnames_option": {"__current_case__": 1, "header": "N", "list": ["3"]}, "cut_element": "-f", "delimiter": ""}`
dbkey	`"?"`

Step 44: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmpp3xor7px/job_working_directory/000/41/outputs/dataset_8f9a5dc9-e7ed-4f17-9613-ae2b086e2269.dat' -g     '#' 'Number of' '/tmp/tmpp3xor7px/files/6/0/3/dataset_6038b8a1-888c-4aa5-a951-a9458e306ef8.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"93678c3679b911efaec4d19c379fcbf3"`
chromInfo	`"/tmp/tmpp3xor7px/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 6: Estimated genome size - Parameter File:
- step_state: scheduled
Step 7: Database for Busco Lineage:
- step_state: scheduled
Step 8: Lineage:
- step_state: scheduled
Step 9: Name of purged assembly:
- step_state: scheduled
Step 10: Name of un-altered assembly:
- step_state: scheduled

Other invocation details
- history_id
  - 6bf360d012c9e552
- history_state
  - ok
- invocation_id
  - 6bf360d012c9e552
- invocation_state
  - scheduled
- workflow_id
  - 21bad7a097b8e670

gxydevbot · 2024-09-24T13:38:57Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-09-24T14:09:37Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Purging-duplicates-one-haplotype-VGP6b.ga_0

Problems:

Output with path /tmp/tmp5ru2hyl1/Busco on data 36 short summary__c2a1d5d3-2c3a-4acf-ab24-d7644302dcc1 different than expected
Expected text 'C:1.1%[S:1.1%,D:0.0%],F:0.5%,M:98.4%,n:3354' in output ('# BUSCO version is: 5.7.1 
# The lineage dataset is: vertebrata_odb10 (Creation date: 2021-02-19, number of genomes: 67, number of BUSCOs: 3354)
# Summarized benchmarking in BUSCO notation for file /tmp/tmpkmnmodhe/files/7/7/5/dataset_775039e5-1130-47ee-9641-25e782a6c26a.dat
# BUSCO was run in mode: euk_genome_min
# Gene predictor used: miniprot

	***** Results: *****

	C:1.0%[S:1.0%,D:0.0%],F:0.1%,M:98.9%,n:3354,E:2.9%	   
	35	Complete BUSCOs (C)	(of which 1 contain internal stop codons)		   
	34	Complete and single-copy BUSCOs (S)	   
	1	Complete and duplicated BUSCOs (D)	   
	4	Fragmented BUSCOs (F)			   
	3315	Missing BUSCOs (M)			   
	3354	Total BUSCO groups searched		   

Assembly Statistics:
	79	Number of scaffolds
	79	Number of contigs
	1884297	Total length
	0.000%	Percent gaps
	21 KB	Scaffold N50
	21 KB	Contigs N50


Dependencies and versions:
	hmmsearch: 3.1
	bbtools: None
	miniprot_index: 0.13-r248
	miniprot_align: 0.13-r248
	python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0)
	busco: 5.7.1
')

Workflow invocation details

Invocation Messages

Steps

Step 1: Genomescope model parameters:
- step_state: scheduled
Step 2: Pacbio Reads Collection - Trimmed:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types float,float,float,float,float,int  --file '/tmp/tmpkmnmodhe/job_working_directory/000/7/configs/tmp6d28f6on' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpkmnmodhe/files/2/0/4/dataset_204d5527-0bbd-4d50-9716-24c164d46d19.dat' '/tmp/tmpkmnmodhe/job_working_directory/000/7/outputs/dataset_a90d6943-17c0-4d7a-887c-5c31bbec3783.dat'

Exit Code:

```
0
```

Standard Output:

1.5*c3
3*c7
Computing 2 new columns with instructions ['1.5*c3;;', '3*c7;;']
Computed new column values for 100.00% of 1 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "1.5c3"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "3c7"}], "header_lines_select": "no"}`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpkmnmodhe/files/1/7/2/dataset_172a181c-af5f-4329-8317-bb2b03e6eec8.dat' reference.fa && minimap2 -x asm5    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmpkmnmodhe/files/b/7/f/dataset_b7f0ef3a-be7c-43ba-924d-17921d769012.dat' > '/tmp/tmpkmnmodhe/job_working_directory/000/8/outputs/dataset_edf379d8-85f9-465d-b8b0-07a05c4a80e4.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.062*0.98] collected minimizers
[M::mm_idx_gen::0.081*0.98] sorted minimizers
[M::main::0.081*0.98] loaded/built the index for 86 target sequence(s)
[M::mm_mapopt_update::0.084*0.98] mid_occ = 54
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 86
[M::mm_idx_stat::0.086*0.98] distinct minimizers: 156208 (93.94% are singletons); average occurrences: 1.302; average spacing: 9.990; total length: 2031175
[M::worker_pipeline::61.647*0.98] mapped 5789 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -x asm5 --q-occ-frac 0.01 -t 1 reference.fa /tmp/tmpkmnmodhe/files/b/7/f/dataset_b7f0ef3a-be7c-43ba-924d-17921d769012.dat
[M::main] Real time: 61.650 sec; CPU: 60.559 sec; Peak RSS: 0.071 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
alignment_options	`{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "asm5", "fastq_input1": {"values": [{"id": 1, "src": "dce"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "paf"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 2, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

split_fa '/tmp/tmpkmnmodhe/files/1/7/2/dataset_172a181c-af5f-4329-8317-bb2b03e6eec8.dat' > split.fasta

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 1, "functions": "split_fa", "input": {"values": [{"id": 2, "src": "hda"}]}}`

Step 14: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpkmnmodhe/files/b/b/5/dataset_bb52cbf7-fdf5-4b14-b3a7-ccf1d1629974.dat' --out-size c   --tabular > '/tmp/tmpkmnmodhe/job_working_directory/000/10/outputs/dataset_38a2e6df-e74e-46bc-a0fb-89a42a49715b.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 15: Estimated genome size:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 16: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpkmnmodhe/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpkmnmodhe/files/a/9/0/dataset_a90d6943-17c0-4d7a-887c-5c31bbec3783.dat' 'c8' T '/tmp/tmpkmnmodhe/job_working_directory/000/12/outputs/dataset_d4a3e0e0-3173-4da4-b47c-7d6016311e5a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8"`
dbkey	`"?"`
delimiter	`"T"`

Step 17: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpkmnmodhe/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpkmnmodhe/files/a/9/0/dataset_a90d6943-17c0-4d7a-887c-5c31bbec3783.dat' 'c7' T '/tmp/tmpkmnmodhe/job_working_directory/000/13/outputs/dataset_7a11b4c3-ed5c-4eea-ad39-5864bd850493.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 18: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpkmnmodhe/files/d/6/d/dataset_d6d09ae8-a34b-45af-968e-fa76a459db73.dat' reference.fa && minimap2 -DP -k19 -w19 -m200    --min-occ-floor 100 --q-occ-frac 0.01 -m 40  -A 1 -B 19 -O 39,81 -E 3,1 -z 200      -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmpkmnmodhe/files/d/6/d/dataset_d6d09ae8-a34b-45af-968e-fa76a459db73.dat' > '/tmp/tmpkmnmodhe/job_working_directory/000/14/outputs/dataset_c6797a14-17a2-44fe-9e58-bfb8f2a2ee5c.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.078*0.77] collected minimizers
[M::mm_idx_gen::0.105*0.75] sorted minimizers
[M::main::0.105*0.75] loaded/built the index for 86 target sequence(s)
[M::mm_mapopt_update::0.109*0.75] mid_occ = 100
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 86
[M::mm_idx_stat::0.112*0.74] distinct minimizers: 156208 (93.94% are singletons); average occurrences: 1.302; average spacing: 9.990; total length: 2031175
[M::worker_pipeline::1.428*0.91] mapped 86 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -DP -k19 -w19 -m200 --min-occ-floor 100 --q-occ-frac 0.01 -m 40 -A 1 -B 19 -O 39,81 -E 3,1 -z 200 -t 1 reference.fa /tmp/tmpkmnmodhe/files/d/6/d/dataset_d6d09ae8-a34b-45af-968e-fa76a459db73.dat
[M::main] Real time: 1.434 sec; CPU: 1.310 sec; Peak RSS: 0.028 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
alignment_options	`{"A": "1", "B": "19", "E": "3", "E2": "1", "O": "39", "O2": "81", "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": "200", "z2": null}`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "self-homology", "fastq_input1": {"values": [{"id": 9, "src": "hda"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "paf"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": "40", "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": "100", "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 19: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpkmnmodhe/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmpkmnmodhe/files/3/8/a/dataset_38a2e6df-e74e-46bc-a0fb-89a42a49715b.dat' --output='/tmp/tmpkmnmodhe/job_working_directory/000/15/outputs/dataset_cc75a336-deaa-42f5-83d9-bad786164130.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9dcf3ac77a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpkmnmodhe/job_working_directory/000/16/configs/tmpnoezs076' '/tmp/tmpkmnmodhe/files/c/c/7/dataset_cc75a336-deaa-42f5-83d9-bad786164130.dat' > '/tmp/tmpkmnmodhe/job_working_directory/000/16/outputs/dataset_0652d282-5f3f-4839-958a-38e5f77fc07d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac77a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmpkmnmodhe/files/0/6/5/dataset_0652d282-5f3f-4839-958a-38e5f77fc07d.dat > '/tmp/tmpkmnmodhe/job_working_directory/000/17/outputs/dataset_7c4de609-a221-4779-aa8b-a1207eb732ed.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac77a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpkmnmodhe/files/0/6/5/dataset_0652d282-5f3f-4839-958a-38e5f77fc07d.dat" "/tmp/tmpkmnmodhe/job_working_directory/000/18/outputs/dataset_12795cec-7934-4c63-8020-dd9774f5286f.dat" "1" "yes"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac77a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9dcf3ac77a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac77a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1933626", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmpkmnmodhe/job_working_directory/000/43/configs/tmp6k43hvof' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpkmnmodhe/files/1/2/7/dataset_12795cec-7934-4c63-8020-dd9774f5286f.dat' '/tmp/tmpkmnmodhe/job_working_directory/000/43/outputs/dataset_e0e2884a-972b-4ef5-885b-fd640990860a.dat'

Exit Code:

```
0
```

Standard Output:

c3/1933626
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1933626;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 79 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac77a7b11ef92c96fb37557b423"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1933626"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 20: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpkmnmodhe/files/b/b/5/dataset_bb52cbf7-fdf5-4b14-b3a7-ccf1d1629974.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmpkmnmodhe/job_working_directory/000/22/outputs/dataset_9298f6fb-3326-4526-8203-9ab71488a1b5.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 3: Assembly to purge:
- step_state: scheduled

Step 21: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 22: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpkmnmodhe/job_working_directory/000/23/configs/tmpjyw69y0z' '/tmp/tmpkmnmodhe/files/9/2/9/dataset_9298f6fb-3326-4526-8203-9ab71488a1b5.dat' > '/tmp/tmpkmnmodhe/job_working_directory/000/23/outputs/dataset_75785869-1b7f-4fb5-b91a-e58062f350bb.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN{print \"Metric\\tAlternate\"}; {print}; "`
dbkey	`"?"`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gzip -c '/tmp/tmpkmnmodhe/files/e/d/f/dataset_edf379d8-85f9-465d-b8b0-07a05c4a80e4.dat' > '0.gz' && pbcstat -M 500 -f 0.0 -l 0 -p '0.gz' && mv PB.stat depth.stat && calcuts -f 0.1 -l 1 -m 16 -u 48 -d 0 depth.stat > cutoffs.tsv 2>calcuts.log && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/e9bd16ba5ebd/purge_dups/hist_plot.py' --cutoffs cutoffs.tsv --title 'Read depth histogram plot' depth.stat hist.png

Exit Code:

```
0
```

Standard Error:

Program starts
Program finished successfully

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	{"__current_case__": 2, "functions": "pbcstat", "input": {"values": [{"id": 2, "src": "hdca"}]}, "output_options": ["pbcstat_coverage", "pbcstat_wig", "depth_stats", "histogram", "calcuts_cutoff", "calcuts_log"], "pbcstat_options": {"flank": "0", "max_cov": "500", "min_map_qual": null, "min_map_ratio": "0.0", "primary_alignments": true}, "section_calcuts": {"low_depth": "1", "min_depth": "0.1", "ploidy": "-d 0", "transition": "16", "upper_depth": "48"}, "section_hist": {"title": "Read depth histogram plot", "xmax": null, "xmin": null, "ymax": null, "ymin": null}}

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gzip -c '/tmp/tmpkmnmodhe/files/c/6/7/dataset_c6797a14-17a2-44fe-9e58-bfb8f2a2ee5c.dat' > '0.gz' && purge_dups -c '/tmp/tmpkmnmodhe/files/c/c/3/dataset_cc382db5-bcb8-4bda-b187-c2a2d4515d40.dat' -T '/tmp/tmpkmnmodhe/files/e/e/8/dataset_ee8b84b7-53e9-4915-9e07-8299b37accb0.dat' -f 0.8 -a 70 -b 200 -m 500 -M 20000 -l 10000 -E 15000 '0.gz' > dups.bed 2> purge_dups.log

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 0, "coverage": {"values": [{"id": 25, "src": "hda"}]}, "cutoffs": {"values": [{"id": 29, "src": "hda"}]}, "double_chain": {"__current_case__": 1, "chaining_rounds": "one"}, "functions": "purge_dups", "input": {"values": [{"id": 14, "src": "hda"}]}, "log_file": true, "max_extend": "15000", "max_gap": "20000", "min_align": "70", "min_bad": "0.8", "min_chain": "500", "min_chain_score": "10000", "min_match": "200"}`

Step 26: Remove REPEATs from BED:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

grep -P -A 0 -B 0 --no-group-separator -v -i -- 'REPEAT' '/tmp/tmpkmnmodhe/files/4/d/c/dataset_4dc90485-c238-4bad-b55f-0f3f109f342e.dat' > '/tmp/tmpkmnmodhe/job_working_directory/000/26/outputs/dataset_2d352849-9962-44ce-b759-95adbab7b246.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`"-v"`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-P"`
url_paste	`"REPEAT"`

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

get_seqs   -e  -l 10000 -m 0.05 -g 10000 '/tmp/tmpkmnmodhe/files/2/d/3/dataset_2d352849-9962-44ce-b759-95adbab7b246.dat' '/tmp/tmpkmnmodhe/files/1/7/2/dataset_172a181c-af5f-4329-8317-bb2b03e6eec8.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 5, "advanced_options": {"coverage": false, "end_trim": true, "haplotigs": false, "length": "10000", "min_gap": "10000", "min_ratio": "0.05", "split": false}, "bed_input": {"values": [{"id": 32, "src": "hda"}]}, "fasta_input": {"values": [{"id": 2, "src": "hda"}]}, "functions": "get_seqs"}`

Step 28: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p output_files && mkdir -p read-db.meryl && tar -zxf /tmp/tmpkmnmodhe/files/b/e/a/dataset_bea54596-8cb7-4b5a-aa03-e2827c05d587.dat -C read-db.meryl --strip-components=1 && ln -s '/tmp/tmpkmnmodhe/files/7/7/5/dataset_775039e5-1130-47ee-9641-25e782a6c26a.dat' assembly_01.fasta && ln -s '/tmp/tmpkmnmodhe/files/b/b/5/dataset_bb52cbf7-fdf5-4b14-b3a7-ccf1d1629974.dat' assembly_02.fasta && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta output_merqury &> /tmp/tmpkmnmodhe/job_working_directory/000/28/outputs/dataset_0108adcd-18e8-4e9b-9a9e-b7ec0608e1a6.dat && mv output_merqury* output_files && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
label	`"output_merqury"`
mode	`{"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 34, "src": "hda"}]}, "assembly_02": {"values": [{"id": 5, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 3, "src": "hda"}]}, "options": "default"}`
output_add_headers	`false`
output_selector	`["qv", "plots", "stats", "log", "hist"]`

Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpkmnmodhe/files/7/7/5/dataset_775039e5-1130-47ee-9641-25e782a6c26a.dat' --out-size c   --tabular > '/tmp/tmpkmnmodhe/job_working_directory/000/29/outputs/dataset_aa6685a4-72af-4eec-a6d4-835f1317cfd1.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 30: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmpkmnmodhe/files/7/7/5/dataset_775039e5-1130-47ee-9641-25e782a6c26a.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'vertebrata_odb10'  --miniprot  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-09-24 14:08:20 ERROR:	Something went wrong. Results not recorded.
2024-09-24 14:08:20 ERROR:	BUSCO analysis failed!
2024-09-24 14:08:20 ERROR:	Check the logs, read the user guide (https://busco.ezlab.org/busco_userguide.html), and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues

Standard Output:

2024-09-24 13:51:22 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 09/24/2024 13:51:22 *****
2024-09-24 13:51:22 INFO:	Configuring BUSCO with local environment
2024-09-24 13:51:22 INFO:	Running genome mode
2024-09-24 13:51:30 INFO:	Input file is /tmp/tmpkmnmodhe/files/7/7/5/dataset_775039e5-1130-47ee-9641-25e782a6c26a.dat
2024-09-24 13:51:30 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_min
2024-09-24 13:51:30 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_min
2024-09-24 13:51:31 INFO:	Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2021-02-19)
2024-09-24 13:51:31 INFO:	Running 1 job(s) on bbtools, starting at 09/24/2024 13:51:31
2024-09-24 13:51:32 INFO:	[bbtools]	1 of 1 task(s) completed
2024-09-24 13:51:32 INFO:	Running 1 job(s) on miniprot_index, starting at 09/24/2024 13:51:32
2024-09-24 13:51:32 INFO:	[miniprot_index]	1 of 1 task(s) completed
2024-09-24 13:51:32 INFO:	Running 1 job(s) on miniprot_align, starting at 09/24/2024 13:51:32
2024-09-24 14:07:40 INFO:	[miniprot_align]	1 of 1 task(s) completed
2024-09-24 14:07:47 INFO:	***** Run HMMER on gene sequences *****
2024-09-24 14:07:49 INFO:	Running 612 job(s) on hmmsearch, starting at 09/24/2024 14:07:49
2024-09-24 14:07:53 INFO:	[hmmsearch]	62 of 612 task(s) completed
2024-09-24 14:07:57 INFO:	[hmmsearch]	123 of 612 task(s) completed
2024-09-24 14:08:00 INFO:	[hmmsearch]	184 of 612 task(s) completed
2024-09-24 14:08:02 INFO:	[hmmsearch]	245 of 612 task(s) completed
2024-09-24 14:08:05 INFO:	[hmmsearch]	307 of 612 task(s) completed
2024-09-24 14:08:07 INFO:	[hmmsearch]	368 of 612 task(s) completed
2024-09-24 14:08:10 INFO:	[hmmsearch]	429 of 612 task(s) completed
2024-09-24 14:08:12 INFO:	[hmmsearch]	490 of 612 task(s) completed
2024-09-24 14:08:16 INFO:	[hmmsearch]	551 of 612 task(s) completed
2024-09-24 14:08:19 INFO:	[hmmsearch]	612 of 612 task(s) completed
2024-09-24 14:08:20 INFO:	45 exons in total
2024-09-24 14:08:20 WARNING:	1 of 35 Complete matches (2.9%) contain internal stop codons in Miniprot gene predictions
2024-09-24 14:08:20 WARNING:	BUSCO gene predictions from Miniprot have low average identity (0.4699999988079071). You may want to repeat the analysis using the Metaeuk pipeline.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "use_augustus_selector": "miniprot"}}`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "missing", "image", "gff"]`

Step 4: Meryl Database:
- step_state: scheduled

Step 31: Convert purged fasta to gfa:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpkmnmodhe/files/7/7/5/dataset_775039e5-1130-47ee-9641-25e782a6c26a.dat'  -o dataset.gfa --discover-terminal-overlaps 1000 --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 79
Total scaffold length: 1884297
Average scaffold length: 23851.86
Scaffold N50: 21449
Scaffold auN: 34441.92
Scaffold L50: 28
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 79
Total contig length: 1884297
Average contig length: 23851.86
Contig N50: 21449
Contig auN: 34441.92
Contig L50: 28
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 577767:363592:365584:577354
GC content %: 38.70
# soft-masked bases: 0
# segments: 79
Total segment length: 1884297
Average segment length: 23851.86
# gaps: 0
# paths: 79
# edges: 1
Average degree: 0.01
# connected components: 1
Largest connected component length: 71428
# dead ends: 156
# disconnected components: 77
Total length disconnected components: 1812869
# separated components: 78
# bubbles: 0
# circular segments: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 1, "terminal_overlaps_length": "1000", "terminal_overlaps_select": "yes"}}, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 32: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpkmnmodhe/files/7/7/5/dataset_775039e5-1130-47ee-9641-25e782a6c26a.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmpkmnmodhe/job_working_directory/000/32/outputs/dataset_85ed0787-284c-4fba-95d5-d78c08840bef.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 33: merqury_QV:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
input	`{"values": [{"id": 3, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury", "which_dataset": "by_identifier"}`

Step 34: output_merqury.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 35: output_merqury.spectra-asm.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.spectra-asm.fl", "which_dataset": "by_identifier"}`

Step 36: output_merqury.assembly_01.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.assembly_01.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 37: merqury_stats:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
input	`{"values": [{"id": 5, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 38: output_merqury.assembly_02.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.assembly_02.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 39: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpkmnmodhe/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmpkmnmodhe/files/a/a/6/dataset_aa6685a4-72af-4eec-a6d4-835f1317cfd1.dat' --output='/tmp/tmpkmnmodhe/job_working_directory/000/33/outputs/dataset_718de909-00d2-4f58-b3dc-de328028dffe.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9dcf3ac87a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpkmnmodhe/job_working_directory/000/34/configs/tmp83h6d_0q' '/tmp/tmpkmnmodhe/files/7/1/8/dataset_718de909-00d2-4f58-b3dc-de328028dffe.dat' > '/tmp/tmpkmnmodhe/job_working_directory/000/34/outputs/dataset_07b8af1a-1b2b-4de9-98a0-c97a46595a3e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac87a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmpkmnmodhe/files/0/7/b/dataset_07b8af1a-1b2b-4de9-98a0-c97a46595a3e.dat > '/tmp/tmpkmnmodhe/job_working_directory/000/35/outputs/dataset_4b5aeef9-79cc-4c9d-9afe-608437e58eb2.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac87a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpkmnmodhe/files/0/7/b/dataset_07b8af1a-1b2b-4de9-98a0-c97a46595a3e.dat" "/tmp/tmpkmnmodhe/job_working_directory/000/36/outputs/dataset_f2d9cdad-0334-4a32-8104-110ccab1db2e.dat" "1" "yes"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac87a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9dcf3ac87a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac87a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1884297", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmpkmnmodhe/job_working_directory/000/51/configs/tmp1t3dafjt' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpkmnmodhe/files/f/2/d/dataset_f2d9cdad-0334-4a32-8104-110ccab1db2e.dat' '/tmp/tmpkmnmodhe/job_working_directory/000/51/outputs/dataset_e7547b6a-47a5-47bd-b56a-09a1a431708c.dat'

Exit Code:

```
0
```

Standard Output:

c3/1884297
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1884297;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 79 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac87a7b11ef92c96fb37557b423"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1884297"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 40: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpkmnmodhe/job_working_directory/000/38/configs/tmpdicrybqe' '/tmp/tmpkmnmodhe/files/8/5/e/dataset_85ed0787-284c-4fba-95d5-d78c08840bef.dat' > '/tmp/tmpkmnmodhe/job_working_directory/000/38/outputs/dataset_a1430ecb-e283-4c4f-aa7f-cb51b68e2d77.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN{print \"Metric\\tPrimary\"}; {print}; "`
dbkey	`"?"`

Step 5: Assembly to leave alone (For Merqury comparison):
- step_state: scheduled

Step 41: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Primary data:
- step_state: scheduled
Step 2: Alternate data:
- step_state: scheduled

Step 11: Size Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpkmnmodhe/job_working_directory/000/58/configs/tmp2dvz7zgn' && Rscript '/tmp/tmpkmnmodhe/job_working_directory/000/58/configs/tmp2dvz7zgn'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmpkmnmodhe/files/e/4/c/dataset_e4c71634-8205-43ac-8e58-6c9041ba497e.dat', sep='\t', header=TRUE)

names(input)[2] <- "xcol"
names(input)[3] <- "ycol"

    gg_facet = NULL
    gg_factor = aes(colour=factor(factor))

        gg_line = geom_line(size=1, alpha=1, gg_factor)

        color_scale = scale_color_brewer(palette='Set1', direction='1')

    names(input)[1] <- "factor"


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmpkmnmodhe/job_working_directory/000/58/outputs/dataset_7e9ef89c-2d11-471d-8d6e-05b389e9efc1.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac97a7b11ef92c96fb37557b423"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"Scaffold number"`
xplot	`"2"`
ylab	`"Cumulative Size (Mb)"`
yplot	`"3"`

Step 3: Name of primary assembly:
- step_state: scheduled
Step 4: Name of alternate assembly:
- step_state: scheduled

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpkmnmodhe/files/e/7/5/dataset_e7547b6a-47a5-47bd-b56a-09a1a431708c.dat" "/tmp/tmpkmnmodhe/job_working_directory/000/52/outputs/dataset_fd077cdc-089b-42df-a76c-3fc7c4831fd2.dat" "Hap1" "no"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac97a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Hap1"`
iterate	`"no"`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpkmnmodhe/files/e/0/e/dataset_e0e2884a-972b-4ef5-885b-fd640990860a.dat" "/tmp/tmpkmnmodhe/job_working_directory/000/53/outputs/dataset_f262eb75-f854-42ef-b0df-c022c595afd6.dat" "Hap2" "no"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac97a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Hap2"`
iterate	`"no"`

Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpkmnmodhe/files/f/d/0/dataset_fd077cdc-089b-42df-a76c-3fc7c4831fd2.dat' >> '/tmp/tmpkmnmodhe/job_working_directory/000/54/outputs/dataset_822ba844-d8b3-4395-9612-814545c8d896.dat' && cat '/tmp/tmpkmnmodhe/files/f/2/6/dataset_f262eb75-f854-42ef-b0df-c022c595afd6.dat' >> '/tmp/tmpkmnmodhe/job_working_directory/000/54/outputs/dataset_822ba844-d8b3-4395-9612-814545c8d896.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac97a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "inputs2": {"values": [{"id": 88, "src": "hda"}]}}]`

Step 8: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpkmnmodhe/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpkmnmodhe/files/8/2/2/dataset_822ba844-d8b3-4395-9612-814545c8d896.dat' 'c8,c5,c6' T '/tmp/tmpkmnmodhe/job_working_directory/000/55/outputs/dataset_8ecc0339-aa64-4358-be64-52907b77076a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9dcf3ac97a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8,c5,c6"`
dbkey	`"?"`
delimiter	`"T"`

Step 9: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpkmnmodhe/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpkmnmodhe/files/8/2/2/dataset_822ba844-d8b3-4395-9612-814545c8d896.dat' 'c8,c4,c7' T '/tmp/tmpkmnmodhe/job_working_directory/000/56/outputs/dataset_e4c71634-8205-43ac-8e58-6c9041ba497e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9dcf3ac97a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8,c4,c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 10: Nx Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpkmnmodhe/job_working_directory/000/57/configs/tmp0jc89519' && Rscript '/tmp/tmpkmnmodhe/job_working_directory/000/57/configs/tmp0jc89519'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmpkmnmodhe/files/8/e/c/dataset_8ecc0339-aa64-4358-be64-52907b77076a.dat', sep='\t', header=TRUE)

names(input)[2] <- "xcol"
names(input)[3] <- "ycol"

    gg_facet = NULL
    gg_factor = aes(colour=factor(factor))

        gg_line = geom_line(size=1, alpha=1, gg_factor)

        color_scale = scale_color_brewer(palette='Set1', direction='1')

    names(input)[1] <- "factor"


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmpkmnmodhe/job_working_directory/000/57/outputs/dataset_479e66b2-8baa-4934-be6c-c3a3c90065c9.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac97a7b11ef92c96fb37557b423"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"x"`
xplot	`"2"`
ylab	`"Nx (Mb)"`
yplot	`"3"`

Step 42: join1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpkmnmodhe/galaxy-dev/tools/filters/join.py' '/tmp/tmpkmnmodhe/files/a/1/4/dataset_a1430ecb-e283-4c4f-aa7f-cb51b68e2d77.dat' '/tmp/tmpkmnmodhe/files/7/5/7/dataset_75785869-1b7f-4fb5-b91a-e58062f350bb.dat' 1 1 '/tmp/tmpkmnmodhe/job_working_directory/000/39/outputs/dataset_16990360-7393-4afe-b1e3-051d01e06c80.dat' -u -p --index_depth=3 --buffer=50000000 --fill_options_file=/tmp/tmpkmnmodhe/job_working_directory/000/39/configs/tmp8amuau57

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
field1	`"1"`
field2	`"1"`
fill_empty_columns	`{"__current_case__": 1, "do_fill_empty_columns": {"__current_case__": 0, "column_fill_type": "single_fill_value", "fill_value": "."}, "fill_columns_by": "fill_unjoined_only", "fill_empty_columns_switch": "fill_empty"}`
header	`""`
partial	`"-p"`
unmatched	`"-u"`

Step 43: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cut --complement -f '3' '/tmp/tmpkmnmodhe/files/1/6/9/dataset_16990360-7393-4afe-b1e3-051d01e06c80.dat' > '/tmp/tmpkmnmodhe/job_working_directory/000/40/outputs/dataset_857208d5-9cc2-4aab-806b-dfd8af8044fe.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
complement	`"--complement"`
cut_type_options	`{"__current_case__": 0, "colnames_option": {"__current_case__": 1, "header": "N", "list": ["3"]}, "cut_element": "-f", "delimiter": ""}`
dbkey	`"?"`

Step 44: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmpkmnmodhe/job_working_directory/000/41/outputs/dataset_49351a6d-6507-4064-8924-8f6fde5adf7c.dat' -g     '#' 'Number of' '/tmp/tmpkmnmodhe/files/8/5/7/dataset_857208d5-9cc2-4aab-806b-dfd8af8044fe.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"9dcf3ac67a7b11ef92c96fb37557b423"`
chromInfo	`"/tmp/tmpkmnmodhe/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 6: Estimated genome size - Parameter File:
- step_state: scheduled
Step 7: Database for Busco Lineage:
- step_state: scheduled
Step 8: Lineage:
- step_state: scheduled
Step 9: Name of purged assembly:
- step_state: scheduled
Step 10: Name of un-altered assembly:
- step_state: scheduled

Other invocation details
- history_id
  - 668876cedce3f665
- history_state
  - ok
- invocation_id
  - 668876cedce3f665
- invocation_state
  - scheduled
- workflow_id
  - 323aa54ccc56b942

gxydevbot · 2024-10-14T04:30:32Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-10-14T04:58:13Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Purging-duplicates-one-haplotype-VGP6b.ga_0

Problems:

Output with path /tmp/tmpepw5stva/Busco on data 36 short summary__7e0578d6-a609-48d0-b2a7-1b3530606c83 different than expected
Expected text 'C:1.1%[S:1.1%,D:0.0%],F:0.5%,M:98.4%,n:3354' in output ('# BUSCO version is: 5.7.1 
# The lineage dataset is: vertebrata_odb10 (Creation date: 2021-02-19, number of genomes: 67, number of BUSCOs: 3354)
# Summarized benchmarking in BUSCO notation for file /tmp/tmp8qg_qx42/files/9/4/0/dataset_9406770f-a52f-4091-a34f-268ed6af19d1.dat
# BUSCO was run in mode: euk_genome_min
# Gene predictor used: miniprot

	***** Results: *****

	C:1.0%[S:1.0%,D:0.0%],F:0.1%,M:98.9%,n:3354,E:2.9%	   
	35	Complete BUSCOs (C)	(of which 1 contain internal stop codons)		   
	34	Complete and single-copy BUSCOs (S)	   
	1	Complete and duplicated BUSCOs (D)	   
	4	Fragmented BUSCOs (F)			   
	3315	Missing BUSCOs (M)			   
	3354	Total BUSCO groups searched		   

Assembly Statistics:
	79	Number of scaffolds
	79	Number of contigs
	1884297	Total length
	0.000%	Percent gaps
	21 KB	Scaffold N50
	21 KB	Contigs N50


Dependencies and versions:
	hmmsearch: 3.1
	bbtools: None
	miniprot_index: 0.13-r248
	miniprot_align: 0.13-r248
	python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0)
	busco: 5.7.1
')

Workflow invocation details

Invocation Messages

Steps

Step 1: Genomescope model parameters:
- step_state: scheduled
Step 2: Pacbio Reads Collection - Trimmed:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types float,float,float,float,float,int  --file '/tmp/tmp8qg_qx42/job_working_directory/000/7/configs/tmprnzm5qb1' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp8qg_qx42/files/3/f/3/dataset_3f39845b-e6bc-4895-b1e9-012e86846e35.dat' '/tmp/tmp8qg_qx42/job_working_directory/000/7/outputs/dataset_59bded3e-d538-44ab-ab6c-067cda7e0b58.dat'

Exit Code:

```
0
```

Standard Output:

1.5*c3
3*c7
Computing 2 new columns with instructions ['1.5*c3;;', '3*c7;;']
Computed new column values for 100.00% of 1 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "1.5c3"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "3c7"}], "header_lines_select": "no"}`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmp8qg_qx42/files/8/4/3/dataset_843d5500-0660-46a3-b77e-c93ef6a2865f.dat' reference.fa && minimap2 -x asm5    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmp8qg_qx42/files/d/c/b/dataset_dcb522ad-83d4-4088-8112-bee11bbc8de0.dat' > '/tmp/tmp8qg_qx42/job_working_directory/000/8/outputs/dataset_ccbe30f7-0933-4225-953a-e910ca902046.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.058*0.99] collected minimizers
[M::mm_idx_gen::0.077*0.97] sorted minimizers
[M::main::0.077*0.97] loaded/built the index for 86 target sequence(s)
[M::mm_mapopt_update::0.080*0.97] mid_occ = 54
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 86
[M::mm_idx_stat::0.082*0.97] distinct minimizers: 156208 (93.94% are singletons); average occurrences: 1.302; average spacing: 9.990; total length: 2031175
[M::worker_pipeline::62.241*0.97] mapped 5789 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -x asm5 --q-occ-frac 0.01 -t 1 reference.fa /tmp/tmp8qg_qx42/files/d/c/b/dataset_dcb522ad-83d4-4088-8112-bee11bbc8de0.dat
[M::main] Real time: 62.243 sec; CPU: 60.543 sec; Peak RSS: 0.071 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
alignment_options	`{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "asm5", "fastq_input1": {"values": [{"id": 1, "src": "dce"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "paf"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 2, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

split_fa '/tmp/tmp8qg_qx42/files/8/4/3/dataset_843d5500-0660-46a3-b77e-c93ef6a2865f.dat' > split.fasta

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 1, "functions": "split_fa", "input": {"values": [{"id": 2, "src": "hda"}]}}`

Step 14: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp8qg_qx42/files/e/3/2/dataset_e32bd55f-c1e9-458f-a310-bbdb22e28fec.dat' --out-size c   --tabular > '/tmp/tmp8qg_qx42/job_working_directory/000/10/outputs/dataset_aecd381c-adfd-4a56-a9df-ee48d5656125.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 15: Estimated genome size:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 16: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp8qg_qx42/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp8qg_qx42/files/5/9/b/dataset_59bded3e-d538-44ab-ab6c-067cda7e0b58.dat' 'c8' T '/tmp/tmp8qg_qx42/job_working_directory/000/12/outputs/dataset_a3e5b404-af07-44e0-a23c-37c8c61e4bcf.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8"`
dbkey	`"?"`
delimiter	`"T"`

Step 17: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp8qg_qx42/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp8qg_qx42/files/5/9/b/dataset_59bded3e-d538-44ab-ab6c-067cda7e0b58.dat' 'c7' T '/tmp/tmp8qg_qx42/job_working_directory/000/13/outputs/dataset_9374a3dc-54bf-4dfc-bd65-d3e8e101e6cf.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 18: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmp8qg_qx42/files/7/3/6/dataset_736066bb-9d16-458f-9e01-046a7a6ce932.dat' reference.fa && minimap2 -DP -k19 -w19 -m200    --min-occ-floor 100 --q-occ-frac 0.01 -m 40  -A 1 -B 19 -O 39,81 -E 3,1 -z 200      -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmp8qg_qx42/files/7/3/6/dataset_736066bb-9d16-458f-9e01-046a7a6ce932.dat' > '/tmp/tmp8qg_qx42/job_working_directory/000/14/outputs/dataset_5d3e6db8-7243-4033-b91b-cbe24cace702.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.054*1.01] collected minimizers
[M::mm_idx_gen::0.070*1.01] sorted minimizers
[M::main::0.070*1.01] loaded/built the index for 86 target sequence(s)
[M::mm_mapopt_update::0.073*1.00] mid_occ = 100
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 86
[M::mm_idx_stat::0.075*1.00] distinct minimizers: 156208 (93.94% are singletons); average occurrences: 1.302; average spacing: 9.990; total length: 2031175
[M::worker_pipeline::1.365*0.95] mapped 86 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -DP -k19 -w19 -m200 --min-occ-floor 100 --q-occ-frac 0.01 -m 40 -A 1 -B 19 -O 39,81 -E 3,1 -z 200 -t 1 reference.fa /tmp/tmp8qg_qx42/files/7/3/6/dataset_736066bb-9d16-458f-9e01-046a7a6ce932.dat
[M::main] Real time: 1.370 sec; CPU: 1.296 sec; Peak RSS: 0.028 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
alignment_options	`{"A": "1", "B": "19", "E": "3", "E2": "1", "O": "39", "O2": "81", "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": "200", "z2": null}`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "self-homology", "fastq_input1": {"values": [{"id": 9, "src": "hda"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "paf"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": "40", "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": "100", "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 19: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp8qg_qx42/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmp8qg_qx42/files/a/e/c/dataset_aecd381c-adfd-4a56-a9df-ee48d5656125.dat' --output='/tmp/tmp8qg_qx42/job_working_directory/000/15/outputs/dataset_2502ac0a-6f06-4431-b7c5-336d417a74a4.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f0a7670f89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp8qg_qx42/job_working_directory/000/16/configs/tmp5z82ksk7' '/tmp/tmp8qg_qx42/files/2/5/0/dataset_2502ac0a-6f06-4431-b7c5-336d417a74a4.dat' > '/tmp/tmp8qg_qx42/job_working_directory/000/16/outputs/dataset_9ea79773-f273-44e9-8c78-d3b23aac6e6c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670f89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmp8qg_qx42/files/9/e/a/dataset_9ea79773-f273-44e9-8c78-d3b23aac6e6c.dat > '/tmp/tmp8qg_qx42/job_working_directory/000/17/outputs/dataset_3fba3f29-5413-4d84-918b-10c570487135.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670f89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmp8qg_qx42/files/9/e/a/dataset_9ea79773-f273-44e9-8c78-d3b23aac6e6c.dat" "/tmp/tmp8qg_qx42/job_working_directory/000/18/outputs/dataset_a16dd479-96fc-462f-823b-ddf56fe4bbbc.dat" "1" "yes"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670f89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f0a7670f89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670f89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1933626", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmp8qg_qx42/job_working_directory/000/43/configs/tmp8ja9u0rd' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp8qg_qx42/files/a/1/6/dataset_a16dd479-96fc-462f-823b-ddf56fe4bbbc.dat' '/tmp/tmp8qg_qx42/job_working_directory/000/43/outputs/dataset_8e61dd2f-b879-471e-ac4b-fd7cbfadd367.dat'

Exit Code:

```
0
```

Standard Output:

c3/1933626
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1933626;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 79 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670f89e511efb6216045bdb31ffc"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1933626"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 20: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp8qg_qx42/files/e/3/2/dataset_e32bd55f-c1e9-458f-a310-bbdb22e28fec.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmp8qg_qx42/job_working_directory/000/22/outputs/dataset_b4fcee2d-cb6b-469b-af25-723ac8691464.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 3: Assembly to purge:
- step_state: scheduled

Step 21: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 22: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp8qg_qx42/job_working_directory/000/23/configs/tmpanewil04' '/tmp/tmp8qg_qx42/files/b/4/f/dataset_b4fcee2d-cb6b-469b-af25-723ac8691464.dat' > '/tmp/tmp8qg_qx42/job_working_directory/000/23/outputs/dataset_e2da62d2-bee7-433b-a922-4194f4ee3ece.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN{print \"Metric\\tAlternate\"}; {print}; "`
dbkey	`"?"`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gzip -c '/tmp/tmp8qg_qx42/files/c/c/b/dataset_ccbe30f7-0933-4225-953a-e910ca902046.dat' > '0.gz' && pbcstat -M 500 -f 0.0 -l 0 -p '0.gz' && mv PB.stat depth.stat && calcuts -f 0.1 -l 1 -m 16 -u 48 -d 0 depth.stat > cutoffs.tsv 2>calcuts.log && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/e9bd16ba5ebd/purge_dups/hist_plot.py' --cutoffs cutoffs.tsv --title 'Read depth histogram plot' depth.stat hist.png

Exit Code:

```
0
```

Standard Error:

Program starts
Program finished successfully

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	{"__current_case__": 2, "functions": "pbcstat", "input": {"values": [{"id": 2, "src": "hdca"}]}, "output_options": ["pbcstat_coverage", "pbcstat_wig", "depth_stats", "histogram", "calcuts_cutoff", "calcuts_log"], "pbcstat_options": {"flank": "0", "max_cov": "500", "min_map_qual": null, "min_map_ratio": "0.0", "primary_alignments": true}, "section_calcuts": {"low_depth": "1", "min_depth": "0.1", "ploidy": "-d 0", "transition": "16", "upper_depth": "48"}, "section_hist": {"title": "Read depth histogram plot", "xmax": null, "xmin": null, "ymax": null, "ymin": null}}

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gzip -c '/tmp/tmp8qg_qx42/files/5/d/3/dataset_5d3e6db8-7243-4033-b91b-cbe24cace702.dat' > '0.gz' && purge_dups -c '/tmp/tmp8qg_qx42/files/2/b/e/dataset_2bed0bcc-0d04-46a6-8ae7-cf22451af973.dat' -T '/tmp/tmp8qg_qx42/files/2/6/5/dataset_265d2fcb-346f-41f9-91f0-2126eac9f524.dat' -f 0.8 -a 70 -b 200 -m 500 -M 20000 -l 10000 -E 15000 '0.gz' > dups.bed 2> purge_dups.log

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 0, "coverage": {"values": [{"id": 25, "src": "hda"}]}, "cutoffs": {"values": [{"id": 29, "src": "hda"}]}, "double_chain": {"__current_case__": 1, "chaining_rounds": "one"}, "functions": "purge_dups", "input": {"values": [{"id": 14, "src": "hda"}]}, "log_file": true, "max_extend": "15000", "max_gap": "20000", "min_align": "70", "min_bad": "0.8", "min_chain": "500", "min_chain_score": "10000", "min_match": "200"}`

Step 26: Remove REPEATs from BED:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

grep -P -A 0 -B 0 --no-group-separator -v -i -- 'REPEAT' '/tmp/tmp8qg_qx42/files/a/0/3/dataset_a03b167b-7adb-41e4-8ee6-93054beffd1d.dat' > '/tmp/tmp8qg_qx42/job_working_directory/000/26/outputs/dataset_d5746ecd-c3f9-4202-8464-03f38fd693da.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`"-v"`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-P"`
url_paste	`"REPEAT"`

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

get_seqs   -e  -l 10000 -m 0.05 -g 10000 '/tmp/tmp8qg_qx42/files/d/5/7/dataset_d5746ecd-c3f9-4202-8464-03f38fd693da.dat' '/tmp/tmp8qg_qx42/files/8/4/3/dataset_843d5500-0660-46a3-b77e-c93ef6a2865f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 5, "advanced_options": {"coverage": false, "end_trim": true, "haplotigs": false, "length": "10000", "min_gap": "10000", "min_ratio": "0.05", "split": false}, "bed_input": {"values": [{"id": 32, "src": "hda"}]}, "fasta_input": {"values": [{"id": 2, "src": "hda"}]}, "functions": "get_seqs"}`

Step 28: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p output_files && mkdir -p read-db.meryl && tar -zxf /tmp/tmp8qg_qx42/files/9/0/b/dataset_90b5fd87-b238-40dc-b41e-42e151c3ab71.dat -C read-db.meryl --strip-components=1 && ln -s '/tmp/tmp8qg_qx42/files/9/4/0/dataset_9406770f-a52f-4091-a34f-268ed6af19d1.dat' assembly_01.fasta && ln -s '/tmp/tmp8qg_qx42/files/e/3/2/dataset_e32bd55f-c1e9-458f-a310-bbdb22e28fec.dat' assembly_02.fasta && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta output_merqury &> /tmp/tmp8qg_qx42/job_working_directory/000/28/outputs/dataset_601ed52c-6b5b-4056-9204-151191ca78a3.dat && mv output_merqury* output_files && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
label	`"output_merqury"`
mode	`{"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 34, "src": "hda"}]}, "assembly_02": {"values": [{"id": 5, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 3, "src": "hda"}]}, "options": "default"}`
output_add_headers	`false`
output_selector	`["qv", "plots", "stats", "log", "hist"]`

Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp8qg_qx42/files/9/4/0/dataset_9406770f-a52f-4091-a34f-268ed6af19d1.dat' --out-size c   --tabular > '/tmp/tmp8qg_qx42/job_working_directory/000/29/outputs/dataset_416a5b98-4fce-45c7-a795-1c6c25c0ff9b.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 30: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.7.1+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmp8qg_qx42/files/9/4/0/dataset_9406770f-a52f-4091-a34f-268ed6af19d1.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'vertebrata_odb10'  --miniprot  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-10-14 04:56:58 ERROR:	Something went wrong. Results not recorded.
2024-10-14 04:56:58 ERROR:	BUSCO analysis failed!
2024-10-14 04:56:58 ERROR:	Check the logs, read the user guide (https://busco.ezlab.org/busco_userguide.html), and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues

Standard Output:

2024-10-14 04:40:07 INFO:	***** Start a BUSCO v5.7.1 analysis, current time: 10/14/2024 04:40:07 *****
2024-10-14 04:40:07 INFO:	Configuring BUSCO with local environment
2024-10-14 04:40:07 INFO:	Running genome mode
2024-10-14 04:40:09 INFO:	Input file is /tmp/tmp8qg_qx42/files/9/4/0/dataset_9406770f-a52f-4091-a34f-268ed6af19d1.dat
2024-10-14 04:40:09 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_min
2024-10-14 04:40:09 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_min
2024-10-14 04:40:09 INFO:	Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2021-02-19)
2024-10-14 04:40:09 INFO:	Running 1 job(s) on bbtools, starting at 10/14/2024 04:40:09
2024-10-14 04:40:11 INFO:	[bbtools]	1 of 1 task(s) completed
2024-10-14 04:40:11 INFO:	Running 1 job(s) on miniprot_index, starting at 10/14/2024 04:40:11
2024-10-14 04:40:12 INFO:	[miniprot_index]	1 of 1 task(s) completed
2024-10-14 04:40:12 INFO:	Running 1 job(s) on miniprot_align, starting at 10/14/2024 04:40:12
2024-10-14 04:56:20 INFO:	[miniprot_align]	1 of 1 task(s) completed
2024-10-14 04:56:25 INFO:	***** Run HMMER on gene sequences *****
2024-10-14 04:56:26 INFO:	Running 612 job(s) on hmmsearch, starting at 10/14/2024 04:56:26
2024-10-14 04:56:30 INFO:	[hmmsearch]	62 of 612 task(s) completed
2024-10-14 04:56:34 INFO:	[hmmsearch]	123 of 612 task(s) completed
2024-10-14 04:56:36 INFO:	[hmmsearch]	184 of 612 task(s) completed
2024-10-14 04:56:39 INFO:	[hmmsearch]	245 of 612 task(s) completed
2024-10-14 04:56:42 INFO:	[hmmsearch]	307 of 612 task(s) completed
2024-10-14 04:56:45 INFO:	[hmmsearch]	368 of 612 task(s) completed
2024-10-14 04:56:48 INFO:	[hmmsearch]	429 of 612 task(s) completed
2024-10-14 04:56:50 INFO:	[hmmsearch]	490 of 612 task(s) completed
2024-10-14 04:56:54 INFO:	[hmmsearch]	551 of 612 task(s) completed
2024-10-14 04:56:58 INFO:	[hmmsearch]	612 of 612 task(s) completed
2024-10-14 04:56:58 INFO:	45 exons in total
2024-10-14 04:56:58 WARNING:	1 of 35 Complete matches (2.9%) contain internal stop codons in Miniprot gene predictions
2024-10-14 04:56:58 WARNING:	BUSCO gene predictions from Miniprot have low average identity (0.4699999988079071). You may want to repeat the analysis using the Metaeuk pipeline.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "use_augustus_selector": "miniprot"}}`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "missing", "image", "gff"]`

Step 4: Meryl Database:
- step_state: scheduled

Step 31: Convert purged fasta to gfa:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp8qg_qx42/files/9/4/0/dataset_9406770f-a52f-4091-a34f-268ed6af19d1.dat'   -o dataset.gfa --discover-terminal-overlaps 1000 --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 79
Total scaffold length: 1884297
Average scaffold length: 23851.86
Scaffold N50: 21449
Scaffold auN: 34441.92
Scaffold L50: 28
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 79
Total contig length: 1884297
Average contig length: 23851.86
Contig N50: 21449
Contig auN: 34441.92
Contig L50: 28
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 577767:363592:365584:577354
GC content %: 38.70
# soft-masked bases: 0
# segments: 79
Total segment length: 1884297
Average segment length: 23851.86
# gaps: 0
# paths: 79
# edges: 1
Average degree: 0.01
# connected components: 1
Largest connected component length: 71428
# dead ends: 156
# disconnected components: 77
Total length disconnected components: 1812869
# separated components: 78
# bubbles: 0
# circular segments: 0
# circular paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 1, "terminal_overlaps_length": "1000", "terminal_overlaps_select": "yes"}}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 32: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp8qg_qx42/files/9/4/0/dataset_9406770f-a52f-4091-a34f-268ed6af19d1.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmp8qg_qx42/job_working_directory/000/32/outputs/dataset_9abdb506-02f8-4f04-a370-1d14040d65e7.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 33: merqury_QV:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
input	`{"values": [{"id": 3, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury", "which_dataset": "by_identifier"}`

Step 34: output_merqury.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 35: output_merqury.spectra-asm.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.spectra-asm.fl", "which_dataset": "by_identifier"}`

Step 36: output_merqury.assembly_01.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.assembly_01.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 37: merqury_stats:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
input	`{"values": [{"id": 5, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 38: output_merqury.assembly_02.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.assembly_02.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 39: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp8qg_qx42/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmp8qg_qx42/files/4/1/6/dataset_416a5b98-4fce-45c7-a795-1c6c25c0ff9b.dat' --output='/tmp/tmp8qg_qx42/job_working_directory/000/33/outputs/dataset_a686fca2-4d1c-41f2-9978-cf0d31ef54a3.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f0a7671089e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp8qg_qx42/job_working_directory/000/34/configs/tmpo8d9lqhd' '/tmp/tmp8qg_qx42/files/a/6/8/dataset_a686fca2-4d1c-41f2-9978-cf0d31ef54a3.dat' > '/tmp/tmp8qg_qx42/job_working_directory/000/34/outputs/dataset_f3481563-ae7d-4955-91ea-d8a7dbb9e4ad.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7671089e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmp8qg_qx42/files/f/3/4/dataset_f3481563-ae7d-4955-91ea-d8a7dbb9e4ad.dat > '/tmp/tmp8qg_qx42/job_working_directory/000/35/outputs/dataset_879da5c0-f0d1-4991-9da8-03d2fbf29180.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7671089e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmp8qg_qx42/files/f/3/4/dataset_f3481563-ae7d-4955-91ea-d8a7dbb9e4ad.dat" "/tmp/tmp8qg_qx42/job_working_directory/000/36/outputs/dataset_5cf6b01f-742f-451a-aefa-d3715c91e314.dat" "1" "yes"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7671089e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f0a7671089e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7671089e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1884297", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmp8qg_qx42/job_working_directory/000/45/configs/tmpgqylyqff' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp8qg_qx42/files/5/c/f/dataset_5cf6b01f-742f-451a-aefa-d3715c91e314.dat' '/tmp/tmp8qg_qx42/job_working_directory/000/45/outputs/dataset_81fda01a-ef03-435e-abb4-c33915e510b9.dat'

Exit Code:

```
0
```

Standard Output:

c3/1884297
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1884297;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 79 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7671089e511efb6216045bdb31ffc"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1884297"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 40: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp8qg_qx42/job_working_directory/000/38/configs/tmpph0hy99g' '/tmp/tmp8qg_qx42/files/9/a/b/dataset_9abdb506-02f8-4f04-a370-1d14040d65e7.dat' > '/tmp/tmp8qg_qx42/job_working_directory/000/38/outputs/dataset_b3d090da-a87c-4c04-bd57-b2a9b072b8c5.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN{print \"Metric\\tPrimary\"}; {print}; "`
dbkey	`"?"`

Step 5: Assembly to leave alone (For Merqury comparison):
- step_state: scheduled

Step 41: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Primary data:
- step_state: scheduled
Step 2: Alternate data:
- step_state: scheduled

Step 11: Size Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp8qg_qx42/job_working_directory/000/52/configs/tmpds7ekpt3' && Rscript '/tmp/tmp8qg_qx42/job_working_directory/000/52/configs/tmpds7ekpt3'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmp8qg_qx42/files/0/4/1/dataset_04162fda-db24-430f-bda1-d3c0e51b3784.dat', sep='\t', header=TRUE)

names(input)[2] <- "xcol"
names(input)[3] <- "ycol"

    gg_facet = NULL
    gg_factor = aes(colour=factor(factor))

        gg_line = geom_line(size=1, alpha=1, gg_factor)

        color_scale = scale_color_brewer(palette='Set1', direction='1')

    names(input)[1] <- "factor"


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmp8qg_qx42/job_working_directory/000/52/outputs/dataset_22038ef5-8f67-4a3b-9fd6-32091b6ee4c1.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7671189e511efb6216045bdb31ffc"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"Scaffold number"`
xplot	`"2"`
ylab	`"Cumulative Size (Mb)"`
yplot	`"3"`

Step 3: Name of primary assembly:
- step_state: scheduled
Step 4: Name of alternate assembly:
- step_state: scheduled

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmp8qg_qx42/files/8/1/f/dataset_81fda01a-ef03-435e-abb4-c33915e510b9.dat" "/tmp/tmp8qg_qx42/job_working_directory/000/46/outputs/dataset_da4ca565-3441-4c43-8662-61041c5562d7.dat" "Hap1" "no"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7671189e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Hap1"`
iterate	`"no"`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmp8qg_qx42/files/8/e/6/dataset_8e61dd2f-b879-471e-ac4b-fd7cbfadd367.dat" "/tmp/tmp8qg_qx42/job_working_directory/000/47/outputs/dataset_4561094d-8ec5-49f6-96fe-3cae4f8217eb.dat" "Hap2" "no"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7671189e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Hap2"`
iterate	`"no"`

Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp8qg_qx42/files/d/a/4/dataset_da4ca565-3441-4c43-8662-61041c5562d7.dat' >> '/tmp/tmp8qg_qx42/job_working_directory/000/48/outputs/dataset_f911d11b-9016-49d2-8fc8-8091bd6ebae5.dat' && cat '/tmp/tmp8qg_qx42/files/4/5/6/dataset_4561094d-8ec5-49f6-96fe-3cae4f8217eb.dat' >> '/tmp/tmp8qg_qx42/job_working_directory/000/48/outputs/dataset_f911d11b-9016-49d2-8fc8-8091bd6ebae5.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7671189e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "inputs2": {"values": [{"id": 58, "src": "hda"}]}}]`

Step 8: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp8qg_qx42/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp8qg_qx42/files/f/9/1/dataset_f911d11b-9016-49d2-8fc8-8091bd6ebae5.dat' 'c8,c5,c6' T '/tmp/tmp8qg_qx42/job_working_directory/000/49/outputs/dataset_a299dc8c-f2ff-4403-8a11-1fad07f76bf8.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f0a7671189e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8,c5,c6"`
dbkey	`"?"`
delimiter	`"T"`

Step 9: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp8qg_qx42/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp8qg_qx42/files/f/9/1/dataset_f911d11b-9016-49d2-8fc8-8091bd6ebae5.dat' 'c8,c4,c7' T '/tmp/tmp8qg_qx42/job_working_directory/000/50/outputs/dataset_04162fda-db24-430f-bda1-d3c0e51b3784.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f0a7671189e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8,c4,c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 10: Nx Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp8qg_qx42/job_working_directory/000/51/configs/tmp_a8b0taq' && Rscript '/tmp/tmp8qg_qx42/job_working_directory/000/51/configs/tmp_a8b0taq'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmp8qg_qx42/files/a/2/9/dataset_a299dc8c-f2ff-4403-8a11-1fad07f76bf8.dat', sep='\t', header=TRUE)

names(input)[2] <- "xcol"
names(input)[3] <- "ycol"

    gg_facet = NULL
    gg_factor = aes(colour=factor(factor))

        gg_line = geom_line(size=1, alpha=1, gg_factor)

        color_scale = scale_color_brewer(palette='Set1', direction='1')

    names(input)[1] <- "factor"


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmp8qg_qx42/job_working_directory/000/51/outputs/dataset_cdc99fc9-146e-4bb7-b1f3-fa99a788afec.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7671189e511efb6216045bdb31ffc"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"x"`
xplot	`"2"`
ylab	`"Nx (Mb)"`
yplot	`"3"`

Step 42: join1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp8qg_qx42/galaxy-dev/tools/filters/join.py' '/tmp/tmp8qg_qx42/files/b/3/d/dataset_b3d090da-a87c-4c04-bd57-b2a9b072b8c5.dat' '/tmp/tmp8qg_qx42/files/e/2/d/dataset_e2da62d2-bee7-433b-a922-4194f4ee3ece.dat' 1 1 '/tmp/tmp8qg_qx42/job_working_directory/000/39/outputs/dataset_698be3df-cd16-46e5-a57a-a626a9f76444.dat' -u -p --index_depth=3 --buffer=50000000 --fill_options_file=/tmp/tmp8qg_qx42/job_working_directory/000/39/configs/tmp3uy5_abk

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
field1	`"1"`
field2	`"1"`
fill_empty_columns	`{"__current_case__": 1, "do_fill_empty_columns": {"__current_case__": 0, "column_fill_type": "single_fill_value", "fill_value": "."}, "fill_columns_by": "fill_unjoined_only", "fill_empty_columns_switch": "fill_empty"}`
header	`""`
partial	`"-p"`
unmatched	`"-u"`

Step 43: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cut --complement -f '3' '/tmp/tmp8qg_qx42/files/6/9/8/dataset_698be3df-cd16-46e5-a57a-a626a9f76444.dat' > '/tmp/tmp8qg_qx42/job_working_directory/000/40/outputs/dataset_73f7b039-db67-4aa6-b5a8-71dfd5ae7c57.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
complement	`"--complement"`
cut_type_options	`{"__current_case__": 0, "colnames_option": {"__current_case__": 1, "header": "N", "list": ["3"]}, "cut_element": "-f", "delimiter": ""}`
dbkey	`"?"`

Step 44: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmp8qg_qx42/job_working_directory/000/41/outputs/dataset_3a1af1ac-7652-464a-b189-4d9a9ec25d95.dat' -g     '#' 'Number of' '/tmp/tmp8qg_qx42/files/7/3/f/dataset_73f7b039-db67-4aa6-b5a8-71dfd5ae7c57.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"f0a7670e89e511efb6216045bdb31ffc"`
chromInfo	`"/tmp/tmp8qg_qx42/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 6: Estimated genome size - Parameter File:
- step_state: scheduled
Step 7: Database for Busco Lineage:
- step_state: scheduled
Step 8: Lineage:
- step_state: scheduled
Step 9: Name of purged assembly:
- step_state: scheduled
Step 10: Name of un-altered assembly:
- step_state: scheduled

Other invocation details
- history_id
  - cddf431294e43a2f
- history_state
  - ok
- invocation_id
  - cddf431294e43a2f
- invocation_state
  - scheduled
- workflow_id
  - 47f4d1f02edf8d93

gxydevbot · 2024-11-04T04:25:09Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-11-04T04:55:28Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Purging-duplicates-one-haplotype-VGP6b.ga_0

Problems:

Output with path /tmp/tmp4ilj98d8/Busco on data 36 short summary__3460d040-c6aa-413c-9644-1d2d0540ff56 different than expected
Expected text 'C:1.1%[S:1.1%,D:0.0%],F:0.5%,M:98.4%,n:3354' in output ('# BUSCO version is: 5.8.0 
# The lineage dataset is: vertebrata_odb10 (Creation date: 2021-02-19, number of genomes: 67, number of BUSCOs: 3354)
# Summarized benchmarking in BUSCO notation for file /tmp/tmpk0_rw2_d/files/3/8/7/dataset_387475c8-7ea1-42e3-8cab-9c1ce09c4126.dat
# BUSCO was run in mode: euk_genome_min
# Gene predictor used: miniprot

	***** Results: *****

	C:1.0%[S:1.0%,D:0.0%],F:0.1%,M:98.8%,n:3354,E:2.9%	   
	35	Complete BUSCOs (C)	(of which 1 contain internal stop codons)		   
	34	Complete and single-copy BUSCOs (S)	   
	1	Complete and duplicated BUSCOs (D)	   
	4	Fragmented BUSCOs (F)			   
	3315	Missing BUSCOs (M)			   
	3354	Total BUSCO groups searched		   

Assembly Statistics:
	79	Number of scaffolds
	79	Number of contigs
	1884297	Total length
	0.000%	Percent gaps
	21 KB	Scaffold N50
	21 KB	Contigs N50


Dependencies and versions:
	hmmsearch: 3.4
	bbtools: None
	miniprot_index: 0.13-r248
	miniprot_align: 0.13-r248
	python: sys.version_info(major=3, minor=10, micro=15, releaselevel='final', serial=0)
	busco: 5.8.0
')

Workflow invocation details

Invocation Messages

Steps

Step 1: Genomescope model parameters:
- step_state: scheduled
Step 2: Pacbio Reads Collection - Trimmed:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types float,float,float,float,float,int  --file '/tmp/tmpk0_rw2_d/job_working_directory/000/7/configs/tmpn6a8jqhv' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpk0_rw2_d/files/9/c/8/dataset_9c8b29ac-5071-497b-b56b-53989add88c3.dat' '/tmp/tmpk0_rw2_d/job_working_directory/000/7/outputs/dataset_a1b46c16-1d15-4e55-8a3c-36150a030f99.dat'

Exit Code:

```
0
```

Standard Output:

1.5*c3
3*c7
Computing 2 new columns with instructions ['1.5*c3;;', '3*c7;;']
Computed new column values for 100.00% of 1 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "1.5c3"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "3c7"}], "header_lines_select": "no"}`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpk0_rw2_d/files/0/1/f/dataset_01f0a6d4-1839-4807-a000-1aa80f5d98aa.dat' reference.fa && minimap2 -x asm5    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmpk0_rw2_d/files/f/2/6/dataset_f26c3c05-2421-4706-a9c6-160f9e5112b6.dat' > '/tmp/tmpk0_rw2_d/job_working_directory/000/8/outputs/dataset_20aa6a8c-1536-4e1e-9ee5-ec4c902c5382.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.054*0.94] collected minimizers
[M::mm_idx_gen::0.069*0.95] sorted minimizers
[M::main::0.069*0.95] loaded/built the index for 86 target sequence(s)
[M::mm_mapopt_update::0.071*0.95] mid_occ = 54
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 86
[M::mm_idx_stat::0.073*0.95] distinct minimizers: 156208 (93.94% are singletons); average occurrences: 1.302; average spacing: 9.990; total length: 2031175
[M::worker_pipeline::60.295*0.99] mapped 5789 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -x asm5 --q-occ-frac 0.01 -t 1 reference.fa /tmp/tmpk0_rw2_d/files/f/2/6/dataset_f26c3c05-2421-4706-a9c6-160f9e5112b6.dat
[M::main] Real time: 60.298 sec; CPU: 59.683 sec; Peak RSS: 0.065 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
alignment_options	`{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "asm5", "fastq_input1": {"values": [{"id": 1, "src": "dce"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "paf"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 2, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

split_fa '/tmp/tmpk0_rw2_d/files/0/1/f/dataset_01f0a6d4-1839-4807-a000-1aa80f5d98aa.dat' > split.fasta

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 1, "functions": "split_fa", "input": {"values": [{"id": 2, "src": "hda"}]}}`

Step 14: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpk0_rw2_d/files/8/3/4/dataset_834b43e5-2ece-44f3-891c-900a4b24f1a6.dat' --out-size c   --tabular > '/tmp/tmpk0_rw2_d/job_working_directory/000/10/outputs/dataset_b478e2ac-da26-4b09-9545-faa3bea2b253.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 15: Estimated genome size:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 16: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpk0_rw2_d/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpk0_rw2_d/files/a/1/b/dataset_a1b46c16-1d15-4e55-8a3c-36150a030f99.dat' 'c8' T '/tmp/tmpk0_rw2_d/job_working_directory/000/12/outputs/dataset_746d533b-2a62-49dd-b0ed-15e0682ae50a.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8"`
dbkey	`"?"`
delimiter	`"T"`

Step 17: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpk0_rw2_d/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpk0_rw2_d/files/a/1/b/dataset_a1b46c16-1d15-4e55-8a3c-36150a030f99.dat' 'c7' T '/tmp/tmpk0_rw2_d/job_working_directory/000/13/outputs/dataset_83e37b89-1d4d-4c4b-aa94-6390310136fa.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 18: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpk0_rw2_d/files/7/f/2/dataset_7f2b7363-4995-48f8-a022-767bb9eea1e3.dat' reference.fa && minimap2 -DP -k19 -w19 -m200    --min-occ-floor 100 --q-occ-frac 0.01 -m 40  -A 1 -B 19 -O 39,81 -E 3,1 -z 200      -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmpk0_rw2_d/files/7/f/2/dataset_7f2b7363-4995-48f8-a022-767bb9eea1e3.dat' > '/tmp/tmpk0_rw2_d/job_working_directory/000/14/outputs/dataset_15d3b555-68ec-45be-80ad-fbfaadc1a1a1.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.056*1.01] collected minimizers
[M::mm_idx_gen::0.074*1.01] sorted minimizers
[M::main::0.075*1.00] loaded/built the index for 86 target sequence(s)
[M::mm_mapopt_update::0.078*1.00] mid_occ = 100
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 86
[M::mm_idx_stat::0.080*0.99] distinct minimizers: 156208 (93.94% are singletons); average occurrences: 1.302; average spacing: 9.990; total length: 2031175
[M::worker_pipeline::1.503*0.91] mapped 86 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -DP -k19 -w19 -m200 --min-occ-floor 100 --q-occ-frac 0.01 -m 40 -A 1 -B 19 -O 39,81 -E 3,1 -z 200 -t 1 reference.fa /tmp/tmpk0_rw2_d/files/7/f/2/dataset_7f2b7363-4995-48f8-a022-767bb9eea1e3.dat
[M::main] Real time: 1.508 sec; CPU: 1.370 sec; Peak RSS: 0.023 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
alignment_options	`{"A": "1", "B": "19", "E": "3", "E2": "1", "O": "39", "O2": "81", "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": "200", "z2": null}`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "self-homology", "fastq_input1": {"values": [{"id": 9, "src": "hda"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "paf"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": "40", "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": "100", "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 19: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpk0_rw2_d/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmpk0_rw2_d/files/b/4/7/dataset_b478e2ac-da26-4b09-9545-faa3bea2b253.dat' --output='/tmp/tmpk0_rw2_d/job_working_directory/000/15/outputs/dataset_a7e4d48a-e709-4718-aa76-903f2551acac.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"0f6ac6799a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpk0_rw2_d/job_working_directory/000/16/configs/tmpws014va1' '/tmp/tmpk0_rw2_d/files/a/7/e/dataset_a7e4d48a-e709-4718-aa76-903f2551acac.dat' > '/tmp/tmpk0_rw2_d/job_working_directory/000/16/outputs/dataset_5b6a71dc-ecc9-4972-bf99-895b7504d268.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6799a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmpk0_rw2_d/files/5/b/6/dataset_5b6a71dc-ecc9-4972-bf99-895b7504d268.dat > '/tmp/tmpk0_rw2_d/job_working_directory/000/17/outputs/dataset_dded24fe-f513-44f6-8208-278e08a3af5d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6799a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpk0_rw2_d/files/5/b/6/dataset_5b6a71dc-ecc9-4972-bf99-895b7504d268.dat" "/tmp/tmpk0_rw2_d/job_working_directory/000/18/outputs/dataset_c0f0d42d-177f-4550-a260-1e274208b86e.dat" "1" "yes"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6799a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"0f6ac6799a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6799a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1933626", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmpk0_rw2_d/job_working_directory/000/43/configs/tmphz2p9sog' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpk0_rw2_d/files/c/0/f/dataset_c0f0d42d-177f-4550-a260-1e274208b86e.dat' '/tmp/tmpk0_rw2_d/job_working_directory/000/43/outputs/dataset_9352be80-8c25-4ff3-b4e2-b647499fea4a.dat'

Exit Code:

```
0
```

Standard Output:

c3/1933626
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1933626;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 79 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6799a6611ef83a30df98cf00a6c"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1933626"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 20: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpk0_rw2_d/files/8/3/4/dataset_834b43e5-2ece-44f3-891c-900a4b24f1a6.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmpk0_rw2_d/job_working_directory/000/22/outputs/dataset_db3fc9f3-9c41-4edf-9f76-cae921f1fc85.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 3: Assembly to purge:
- step_state: scheduled

Step 21: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 22: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpk0_rw2_d/job_working_directory/000/23/configs/tmprxcux4ra' '/tmp/tmpk0_rw2_d/files/d/b/3/dataset_db3fc9f3-9c41-4edf-9f76-cae921f1fc85.dat' > '/tmp/tmpk0_rw2_d/job_working_directory/000/23/outputs/dataset_3e784967-d929-472e-8a76-6a2c81e4724e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN{print \"Metric\\tAlternate\"}; {print}; "`
dbkey	`"?"`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gzip -c '/tmp/tmpk0_rw2_d/files/2/0/a/dataset_20aa6a8c-1536-4e1e-9ee5-ec4c902c5382.dat' > '0.gz' && pbcstat -M 500 -f 0.0 -l 0 -p '0.gz' && mv PB.stat depth.stat && calcuts -f 0.1 -l 1 -m 16 -u 48 -d 0 depth.stat > cutoffs.tsv 2>calcuts.log && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/e9bd16ba5ebd/purge_dups/hist_plot.py' --cutoffs cutoffs.tsv --title 'Read depth histogram plot' depth.stat hist.png

Exit Code:

```
0
```

Standard Error:

Program starts
Program finished successfully

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	{"__current_case__": 2, "functions": "pbcstat", "input": {"values": [{"id": 2, "src": "hdca"}]}, "output_options": ["pbcstat_coverage", "pbcstat_wig", "depth_stats", "histogram", "calcuts_cutoff", "calcuts_log"], "pbcstat_options": {"flank": "0", "max_cov": "500", "min_map_qual": null, "min_map_ratio": "0.0", "primary_alignments": true}, "section_calcuts": {"low_depth": "1", "min_depth": "0.1", "ploidy": "-d 0", "transition": "16", "upper_depth": "48"}, "section_hist": {"title": "Read depth histogram plot", "xmax": null, "xmin": null, "ymax": null, "ymin": null}}

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gzip -c '/tmp/tmpk0_rw2_d/files/1/5/d/dataset_15d3b555-68ec-45be-80ad-fbfaadc1a1a1.dat' > '0.gz' && purge_dups -c '/tmp/tmpk0_rw2_d/files/b/9/3/dataset_b9375818-a50b-495b-987c-cc73d28dd4b9.dat' -T '/tmp/tmpk0_rw2_d/files/e/6/4/dataset_e648c90d-a0d7-47c0-a3b9-466b20827a02.dat' -f 0.8 -a 70 -b 200 -m 500 -M 20000 -l 10000 -E 15000 '0.gz' > dups.bed 2> purge_dups.log

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 0, "coverage": {"values": [{"id": 25, "src": "hda"}]}, "cutoffs": {"values": [{"id": 29, "src": "hda"}]}, "double_chain": {"__current_case__": 1, "chaining_rounds": "one"}, "functions": "purge_dups", "input": {"values": [{"id": 14, "src": "hda"}]}, "log_file": true, "max_extend": "15000", "max_gap": "20000", "min_align": "70", "min_bad": "0.8", "min_chain": "500", "min_chain_score": "10000", "min_match": "200"}`

Step 26: Remove REPEATs from BED:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

grep -P -A 0 -B 0 --no-group-separator -v -i -- 'REPEAT' '/tmp/tmpk0_rw2_d/files/f/f/0/dataset_ff00afe1-ac77-40fa-891a-bf2d26acb7c3.dat' > '/tmp/tmpk0_rw2_d/job_working_directory/000/26/outputs/dataset_5fa82546-be6e-43a7-b6c1-9719611f805b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`"-v"`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-P"`
url_paste	`"REPEAT"`

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

get_seqs   -e  -l 10000 -m 0.05 -g 10000 '/tmp/tmpk0_rw2_d/files/5/f/a/dataset_5fa82546-be6e-43a7-b6c1-9719611f805b.dat' '/tmp/tmpk0_rw2_d/files/0/1/f/dataset_01f0a6d4-1839-4807-a000-1aa80f5d98aa.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 5, "advanced_options": {"coverage": false, "end_trim": true, "haplotigs": false, "length": "10000", "min_gap": "10000", "min_ratio": "0.05", "split": false}, "bed_input": {"values": [{"id": 32, "src": "hda"}]}, "fasta_input": {"values": [{"id": 2, "src": "hda"}]}, "functions": "get_seqs"}`

Step 28: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p output_files && mkdir -p read-db.meryl && tar -zxf /tmp/tmpk0_rw2_d/files/4/a/1/dataset_4a14fff6-239a-4f1a-b91c-1c64ad34b004.dat -C read-db.meryl --strip-components=1 && ln -s '/tmp/tmpk0_rw2_d/files/3/8/7/dataset_387475c8-7ea1-42e3-8cab-9c1ce09c4126.dat' assembly_01.fasta && ln -s '/tmp/tmpk0_rw2_d/files/8/3/4/dataset_834b43e5-2ece-44f3-891c-900a4b24f1a6.dat' assembly_02.fasta && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta output_merqury &> /tmp/tmpk0_rw2_d/job_working_directory/000/28/outputs/dataset_a236fba0-9b77-4a90-af1d-8fc152603cf3.dat && mv output_merqury* output_files && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
label	`"output_merqury"`
mode	`{"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 34, "src": "hda"}]}, "assembly_02": {"values": [{"id": 5, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 3, "src": "hda"}]}, "options": "default"}`
output_add_headers	`false`
output_selector	`["qv", "plots", "stats", "log", "hist"]`

Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpk0_rw2_d/files/3/8/7/dataset_387475c8-7ea1-42e3-8cab-9c1ce09c4126.dat' --out-size c   --tabular > '/tmp/tmpk0_rw2_d/job_working_directory/000/29/outputs/dataset_fdc45072-5309-4da0-b31d-b7ce112c17ad.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 30: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmpk0_rw2_d/files/3/8/7/dataset_387475c8-7ea1-42e3-8cab-9c1ce09c4126.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'vertebrata_odb10'  --miniprot  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-11-04 04:54:20 ERROR:	
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-11-04 04:37:31 INFO:	***** Start a BUSCO v5.8.0 analysis, current time: 11/04/2024 04:37:31 *****
2024-11-04 04:37:31 INFO:	Configuring BUSCO with local environment
2024-11-04 04:37:31 INFO:	Running genome mode
2024-11-04 04:37:33 INFO:	Input file is /tmp/tmpk0_rw2_d/files/3/8/7/dataset_387475c8-7ea1-42e3-8cab-9c1ce09c4126.dat
2024-11-04 04:37:33 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_min
2024-11-04 04:37:33 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_min
2024-11-04 04:37:33 INFO:	Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2021-02-19)
2024-11-04 04:37:33 INFO:	Running 1 job(s) on bbtools, starting at 11/04/2024 04:37:33
2024-11-04 04:37:34 INFO:	[bbtools]	1 of 1 task(s) completed
2024-11-04 04:37:34 INFO:	Running 1 job(s) on miniprot_index, starting at 11/04/2024 04:37:34
2024-11-04 04:37:35 INFO:	[miniprot_index]	1 of 1 task(s) completed
2024-11-04 04:37:35 INFO:	Running 1 job(s) on miniprot_align, starting at 11/04/2024 04:37:35
2024-11-04 04:53:30 INFO:	[miniprot_align]	1 of 1 task(s) completed
2024-11-04 04:53:36 INFO:	***** Run HMMER on gene sequences *****
2024-11-04 04:53:37 INFO:	Running 612 job(s) on hmmsearch, starting at 11/04/2024 04:53:37
2024-11-04 04:53:42 INFO:	[hmmsearch]	62 of 612 task(s) completed
2024-11-04 04:53:47 INFO:	[hmmsearch]	123 of 612 task(s) completed
2024-11-04 04:53:51 INFO:	[hmmsearch]	184 of 612 task(s) completed
2024-11-04 04:53:55 INFO:	[hmmsearch]	245 of 612 task(s) completed
2024-11-04 04:53:59 INFO:	[hmmsearch]	307 of 612 task(s) completed
2024-11-04 04:54:02 INFO:	[hmmsearch]	368 of 612 task(s) completed
2024-11-04 04:54:06 INFO:	[hmmsearch]	429 of 612 task(s) completed
2024-11-04 04:54:09 INFO:	[hmmsearch]	490 of 612 task(s) completed
2024-11-04 04:54:12 INFO:	[hmmsearch]	551 of 612 task(s) completed
2024-11-04 04:54:17 INFO:	[hmmsearch]	612 of 612 task(s) completed
2024-11-04 04:54:17 INFO:	45 exons in total
2024-11-04 04:54:17 WARNING:	1 of 35 Complete matches (2.9%) contain internal stop codons in Miniprot gene predictions
2024-11-04 04:54:17 WARNING:	BUSCO gene predictions from Miniprot have low average identity (0.47). You may want to repeat the analysis using the Metaeuk pipeline.
2024-11-04 04:54:17 INFO:	

    -------------------------------------------------------------------------------------------
    |Results from dataset vertebrata_odb10                                                     |
    -------------------------------------------------------------------------------------------
    |C:1.0%[S:1.0%,D:0.0%],F:0.1%,M:98.8%,n:3354,E:2.9%                                        |
    |35    Complete BUSCOs (C)    (of which 1 contain internal stop codons)                    |
    |34    Complete and single-copy BUSCOs (S)                                                 |
    |1    Complete and duplicated BUSCOs (D)                                                   |
    |4    Fragmented BUSCOs (F)                                                                |
    |3315    Missing BUSCOs (M)                                                                |
    |3354    Total BUSCO groups searched                                                       |
    -------------------------------------------------------------------------------------------
2024-11-04 04:54:17 INFO:	BUSCO analysis done with WARNING(s). Total running time: 1004 seconds

***** Summary of warnings: *****
2024-11-04 04:37:33 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_genome_min
2024-11-04 04:37:33 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_genome_min
2024-11-04 04:54:17 WARNING:busco.busco_tools.hmmer	1 of 35 Complete matches (2.9%) contain internal stop codons in Miniprot gene predictions
2024-11-04 04:54:17 WARNING:busco.busco_tools.hmmer	BUSCO gene predictions from Miniprot have low average identity (0.47). You may want to repeat the analysis using the Metaeuk pipeline.

2024-11-04 04:54:17 INFO:	Results written in /tmp/tmpk0_rw2_d/job_working_directory/000/30/working/busco_galaxy
2024-11-04 04:54:17 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-11-04 04:54:17 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 156
drwxr-xr-x 5 1001 127  4096 Nov  4 04:37 busco_sequences
-rw-r--r-- 1 1001 127 74999 Nov  4 04:54 full_table.tsv
drwxr-xr-x 2 1001 127 20480 Nov  4 04:54 hmmer_output
drwxr-xr-x 3 1001 127  4096 Nov  4 04:53 miniprot_output
-rw-r--r-- 1 1001 127 42532 Nov  4 04:54 missing_busco_list.tsv
-rw-r--r-- 1 1001 127  2869 Nov  4 04:54 short_summary.json
-rw-r--r-- 1 1001 127  1051 Nov  4 04:54 short_summary.txt
2024-11-04 04:54:18 INFO:	****************** Start plot generation at 11/04/2024 04:54:18 ******************
2024-11-04 04:54:18 INFO:	Load data ...
2024-11-04 04:54:18 INFO:	Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully
2024-11-04 04:54:18 INFO:	Generate the R code ...
2024-11-04 04:54:18 INFO:	Run the R code ...
2024-11-04 04:54:20 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-11-04 04:54:20 INFO:	Plot generation done. Total running time: 2.221247434616089 seconds
2024-11-04 04:54:20 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "use_augustus_selector": "miniprot"}}`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "missing", "image", "gff"]`

Step 4: Meryl Database:
- step_state: scheduled

Step 31: Convert purged fasta to gfa:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpk0_rw2_d/files/3/8/7/dataset_387475c8-7ea1-42e3-8cab-9c1ce09c4126.dat'   -o dataset.gfa --discover-terminal-overlaps 1000 --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 79
Total scaffold length: 1884297
Average scaffold length: 23851.86
Scaffold N50: 21449
Scaffold auN: 34441.92
Scaffold L50: 28
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 79
Total contig length: 1884297
Average contig length: 23851.86
Contig N50: 21449
Contig auN: 34441.92
Contig L50: 28
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 577767:363592:365584:577354
GC content %: 38.70
# soft-masked bases: 0
# segments: 79
Total segment length: 1884297
Average segment length: 23851.86
# gaps: 0
# paths: 79
# edges: 1
Average degree: 0.01
# connected components: 1
Largest connected component length: 71428
# dead ends: 156
# disconnected components: 77
Total length disconnected components: 1812869
# separated components: 78
# bubbles: 0
# circular segments: 0
# circular paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 1, "terminal_overlaps_length": "1000", "terminal_overlaps_select": "yes"}}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 32: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpk0_rw2_d/files/3/8/7/dataset_387475c8-7ea1-42e3-8cab-9c1ce09c4126.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmpk0_rw2_d/job_working_directory/000/32/outputs/dataset_6487c6cf-03ca-46d1-bf0a-ea2f0d9c0374.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 33: merqury_QV:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
input	`{"values": [{"id": 3, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury", "which_dataset": "by_identifier"}`

Step 34: output_merqury.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 35: output_merqury.spectra-asm.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.spectra-asm.fl", "which_dataset": "by_identifier"}`

Step 36: output_merqury.assembly_01.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.assembly_01.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 37: merqury_stats:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
input	`{"values": [{"id": 5, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 38: output_merqury.assembly_02.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.assembly_02.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 39: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpk0_rw2_d/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmpk0_rw2_d/files/f/d/c/dataset_fdc45072-5309-4da0-b31d-b7ce112c17ad.dat' --output='/tmp/tmpk0_rw2_d/job_working_directory/000/33/outputs/dataset_d9c3e3bd-257b-4aa7-adc3-53534a3a1f4a.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"0f6ac67a9a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpk0_rw2_d/job_working_directory/000/34/configs/tmpzzugsol1' '/tmp/tmpk0_rw2_d/files/d/9/c/dataset_d9c3e3bd-257b-4aa7-adc3-53534a3a1f4a.dat' > '/tmp/tmpk0_rw2_d/job_working_directory/000/34/outputs/dataset_7e21eecd-9858-44a7-8bca-81bc3468b5da.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac67a9a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmpk0_rw2_d/files/7/e/2/dataset_7e21eecd-9858-44a7-8bca-81bc3468b5da.dat > '/tmp/tmpk0_rw2_d/job_working_directory/000/35/outputs/dataset_2d923cab-eae0-4941-8ef6-05c112e385b7.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac67a9a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpk0_rw2_d/files/7/e/2/dataset_7e21eecd-9858-44a7-8bca-81bc3468b5da.dat" "/tmp/tmpk0_rw2_d/job_working_directory/000/36/outputs/dataset_5d87c3bc-1d86-413c-82e6-e3cffd022e73.dat" "1" "yes"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac67a9a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"0f6ac67a9a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac67a9a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1884297", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmpk0_rw2_d/job_working_directory/000/45/configs/tmp1kxk0as1' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpk0_rw2_d/files/5/d/8/dataset_5d87c3bc-1d86-413c-82e6-e3cffd022e73.dat' '/tmp/tmpk0_rw2_d/job_working_directory/000/45/outputs/dataset_e366b787-69f6-498f-b251-f7109e2c103a.dat'

Exit Code:

```
0
```

Standard Output:

c3/1884297
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1884297;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 79 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac67a9a6611ef83a30df98cf00a6c"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1884297"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 40: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpk0_rw2_d/job_working_directory/000/38/configs/tmpvkmeuwka' '/tmp/tmpk0_rw2_d/files/6/4/8/dataset_6487c6cf-03ca-46d1-bf0a-ea2f0d9c0374.dat' > '/tmp/tmpk0_rw2_d/job_working_directory/000/38/outputs/dataset_408e042a-d8f8-40f8-a963-a479156a493f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN{print \"Metric\\tPrimary\"}; {print}; "`
dbkey	`"?"`

Step 5: Assembly to leave alone (For Merqury comparison):
- step_state: scheduled

Step 41: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Primary data:
- step_state: scheduled
Step 2: Alternate data:
- step_state: scheduled

Step 11: Size Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpk0_rw2_d/job_working_directory/000/52/configs/tmpyzdjpdkt' && Rscript '/tmp/tmpk0_rw2_d/job_working_directory/000/52/configs/tmpyzdjpdkt'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmpk0_rw2_d/files/e/f/7/dataset_ef795d79-6454-4bcb-aed8-194344adaf5c.dat', sep='\t', header=TRUE)

names(input)[2] <- "xcol"
names(input)[3] <- "ycol"

    gg_facet = NULL
    gg_factor = aes(colour=factor(factor))

        gg_line = geom_line(size=1, alpha=1, gg_factor)

        color_scale = scale_color_brewer(palette='Set1', direction='1')

    names(input)[1] <- "factor"


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmpk0_rw2_d/job_working_directory/000/52/outputs/dataset_b00dfc3b-1915-4301-baaa-e8afc2e8a759.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac67b9a6611ef83a30df98cf00a6c"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"Scaffold number"`
xplot	`"2"`
ylab	`"Cumulative Size (Mb)"`
yplot	`"3"`

Step 3: Name of primary assembly:
- step_state: scheduled
Step 4: Name of alternate assembly:
- step_state: scheduled

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpk0_rw2_d/files/e/3/6/dataset_e366b787-69f6-498f-b251-f7109e2c103a.dat" "/tmp/tmpk0_rw2_d/job_working_directory/000/46/outputs/dataset_2e8d572e-c57e-46c3-9f47-420cce8fb5d8.dat" "Hap1" "no"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac67b9a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Hap1"`
iterate	`"no"`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpk0_rw2_d/files/9/3/5/dataset_9352be80-8c25-4ff3-b4e2-b647499fea4a.dat" "/tmp/tmpk0_rw2_d/job_working_directory/000/47/outputs/dataset_1f054817-64b1-4d6c-a8de-7adebfaa2c04.dat" "Hap2" "no"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac67b9a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Hap2"`
iterate	`"no"`

Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpk0_rw2_d/files/2/e/8/dataset_2e8d572e-c57e-46c3-9f47-420cce8fb5d8.dat' >> '/tmp/tmpk0_rw2_d/job_working_directory/000/48/outputs/dataset_a6c04604-9658-4da7-b186-848df1444993.dat' && cat '/tmp/tmpk0_rw2_d/files/1/f/0/dataset_1f054817-64b1-4d6c-a8de-7adebfaa2c04.dat' >> '/tmp/tmpk0_rw2_d/job_working_directory/000/48/outputs/dataset_a6c04604-9658-4da7-b186-848df1444993.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac67b9a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "inputs2": {"values": [{"id": 58, "src": "hda"}]}}]`

Step 8: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpk0_rw2_d/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpk0_rw2_d/files/a/6/c/dataset_a6c04604-9658-4da7-b186-848df1444993.dat' 'c8,c5,c6' T '/tmp/tmpk0_rw2_d/job_working_directory/000/49/outputs/dataset_a8a6e42f-3f5b-44f5-9e65-6df5ff9f8359.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"0f6ac67b9a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8,c5,c6"`
dbkey	`"?"`
delimiter	`"T"`

Step 9: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpk0_rw2_d/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpk0_rw2_d/files/a/6/c/dataset_a6c04604-9658-4da7-b186-848df1444993.dat' 'c8,c4,c7' T '/tmp/tmpk0_rw2_d/job_working_directory/000/50/outputs/dataset_ef795d79-6454-4bcb-aed8-194344adaf5c.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"0f6ac67b9a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8,c4,c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 10: Nx Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpk0_rw2_d/job_working_directory/000/51/configs/tmpx_7xomq8' && Rscript '/tmp/tmpk0_rw2_d/job_working_directory/000/51/configs/tmpx_7xomq8'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmpk0_rw2_d/files/a/8/a/dataset_a8a6e42f-3f5b-44f5-9e65-6df5ff9f8359.dat', sep='\t', header=TRUE)

names(input)[2] <- "xcol"
names(input)[3] <- "ycol"

    gg_facet = NULL
    gg_factor = aes(colour=factor(factor))

        gg_line = geom_line(size=1, alpha=1, gg_factor)

        color_scale = scale_color_brewer(palette='Set1', direction='1')

    names(input)[1] <- "factor"


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmpk0_rw2_d/job_working_directory/000/51/outputs/dataset_c8701d6a-14f1-482c-8e31-3bfaeec35258.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac67b9a6611ef83a30df98cf00a6c"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"x"`
xplot	`"2"`
ylab	`"Nx (Mb)"`
yplot	`"3"`

Step 42: join1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpk0_rw2_d/galaxy-dev/tools/filters/join.py' '/tmp/tmpk0_rw2_d/files/4/0/8/dataset_408e042a-d8f8-40f8-a963-a479156a493f.dat' '/tmp/tmpk0_rw2_d/files/3/e/7/dataset_3e784967-d929-472e-8a76-6a2c81e4724e.dat' 1 1 '/tmp/tmpk0_rw2_d/job_working_directory/000/39/outputs/dataset_dd27bf5e-264a-431d-8c31-06fdf6b5d832.dat' -u -p --index_depth=3 --buffer=50000000 --fill_options_file=/tmp/tmpk0_rw2_d/job_working_directory/000/39/configs/tmpvppoluw4

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
field1	`"1"`
field2	`"1"`
fill_empty_columns	`{"__current_case__": 1, "do_fill_empty_columns": {"__current_case__": 0, "column_fill_type": "single_fill_value", "fill_value": "."}, "fill_columns_by": "fill_unjoined_only", "fill_empty_columns_switch": "fill_empty"}`
header	`""`
partial	`"-p"`
unmatched	`"-u"`

Step 43: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cut --complement -f '3' '/tmp/tmpk0_rw2_d/files/d/d/2/dataset_dd27bf5e-264a-431d-8c31-06fdf6b5d832.dat' > '/tmp/tmpk0_rw2_d/job_working_directory/000/40/outputs/dataset_9b496ca4-ded7-4113-83fc-4359a6173441.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
complement	`"--complement"`
cut_type_options	`{"__current_case__": 0, "colnames_option": {"__current_case__": 1, "header": "N", "list": ["3"]}, "cut_element": "-f", "delimiter": ""}`
dbkey	`"?"`

Step 44: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmpk0_rw2_d/job_working_directory/000/41/outputs/dataset_3b75443a-edc4-406a-925a-83c7bfcc16c2.dat' -g     '#' 'Number of' '/tmp/tmpk0_rw2_d/files/9/b/4/dataset_9b496ca4-ded7-4113-83fc-4359a6173441.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"0f6ac6789a6611ef83a30df98cf00a6c"`
chromInfo	`"/tmp/tmpk0_rw2_d/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 6: Estimated genome size - Parameter File:
- step_state: scheduled
Step 7: Database for Busco Lineage:
- step_state: scheduled
Step 8: Lineage:
- step_state: scheduled
Step 9: Name of purged assembly:
- step_state: scheduled
Step 10: Name of un-altered assembly:
- step_state: scheduled

Other invocation details
- history_id
  - a2e82eefc9be1396
- history_state
  - ok
- invocation_id
  - a2e82eefc9be1396
- invocation_state
  - scheduled
- workflow_id
  - 6a681f747cdbc1c0

gxydevbot · 2024-11-11T04:30:42Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-11-11T05:00:26Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Purging-duplicates-one-haplotype-VGP6b.ga_0

Problems:

Output with path /tmp/tmpa3hrpis1/Busco on data 36 short summary__1f3f8aea-d7af-4c26-b5b6-c60ea3d56d97 different than expected
Expected text 'C:1.1%[S:1.1%,D:0.0%],F:0.5%,M:98.4%,n:3354' in output ('# BUSCO version is: 5.8.0 
# The lineage dataset is: vertebrata_odb10 (Creation date: 2021-02-19, number of genomes: 67, number of BUSCOs: 3354)
# Summarized benchmarking in BUSCO notation for file /tmp/tmpxwsyv56g/files/6/e/8/dataset_6e812f4f-453b-450b-a7d1-0fc4d98ef944.dat
# BUSCO was run in mode: euk_genome_min
# Gene predictor used: miniprot

	***** Results: *****

	C:1.0%[S:1.0%,D:0.0%],F:0.1%,M:98.8%,n:3354,E:2.9%	   
	35	Complete BUSCOs (C)	(of which 1 contain internal stop codons)		   
	34	Complete and single-copy BUSCOs (S)	   
	1	Complete and duplicated BUSCOs (D)	   
	4	Fragmented BUSCOs (F)			   
	3315	Missing BUSCOs (M)			   
	3354	Total BUSCO groups searched		   

Assembly Statistics:
	79	Number of scaffolds
	79	Number of contigs
	1884297	Total length
	0.000%	Percent gaps
	21 KB	Scaffold N50
	21 KB	Contigs N50


Dependencies and versions:
	hmmsearch: 3.4
	bbtools: None
	miniprot_index: 0.13-r248
	miniprot_align: 0.13-r248
	python: sys.version_info(major=3, minor=10, micro=15, releaselevel='final', serial=0)
	busco: 5.8.0
')

Workflow invocation details

Invocation Messages

Steps

Step 1: Genomescope model parameters:
- step_state: scheduled
Step 2: Pacbio Reads Collection - Trimmed:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types float,float,float,float,float,int  --file '/tmp/tmpxwsyv56g/job_working_directory/000/7/configs/tmp03clu6e_' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpxwsyv56g/files/4/7/c/dataset_47c13dfa-fb95-454b-86f5-ae09063ef7e8.dat' '/tmp/tmpxwsyv56g/job_working_directory/000/7/outputs/dataset_65b95096-3b81-43eb-8818-ba35f88022dc.dat'

Exit Code:

```
0
```

Standard Output:

1.5*c3
3*c7
Computing 2 new columns with instructions ['1.5*c3;;', '3*c7;;']
Computed new column values for 100.00% of 1 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "1.5c3"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "3c7"}], "header_lines_select": "no"}`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpxwsyv56g/files/8/1/9/dataset_819537ac-dd6b-4de0-944b-569615d46e0d.dat' reference.fa && minimap2 -x asm5    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmpxwsyv56g/files/6/4/4/dataset_644e136a-6939-4fb6-aa45-363410a66878.dat' > '/tmp/tmpxwsyv56g/job_working_directory/000/8/outputs/dataset_cf3bb9eb-5f8c-4f05-84e6-d741c9181da0.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.057*1.01] collected minimizers
[M::mm_idx_gen::0.073*1.01] sorted minimizers
[M::main::0.073*1.01] loaded/built the index for 86 target sequence(s)
[M::mm_mapopt_update::0.076*1.01] mid_occ = 54
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 86
[M::mm_idx_stat::0.078*1.01] distinct minimizers: 156208 (93.94% are singletons); average occurrences: 1.302; average spacing: 9.990; total length: 2031175
[M::worker_pipeline::59.645*0.99] mapped 5789 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -x asm5 --q-occ-frac 0.01 -t 1 reference.fa /tmp/tmpxwsyv56g/files/6/4/4/dataset_644e136a-6939-4fb6-aa45-363410a66878.dat
[M::main] Real time: 59.649 sec; CPU: 59.100 sec; Peak RSS: 0.065 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
alignment_options	`{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "asm5", "fastq_input1": {"values": [{"id": 1, "src": "dce"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "paf"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 2, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

split_fa '/tmp/tmpxwsyv56g/files/8/1/9/dataset_819537ac-dd6b-4de0-944b-569615d46e0d.dat' > split.fasta

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 1, "functions": "split_fa", "input": {"values": [{"id": 2, "src": "hda"}]}}`

Step 14: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpxwsyv56g/files/4/1/c/dataset_41cd89bf-b554-4489-8086-b33bd3487d9e.dat' --out-size c   --tabular > '/tmp/tmpxwsyv56g/job_working_directory/000/10/outputs/dataset_8747d498-215f-4d0a-ac84-eb8bd3d4e2b3.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 15: Estimated genome size:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 16: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpxwsyv56g/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpxwsyv56g/files/6/5/b/dataset_65b95096-3b81-43eb-8818-ba35f88022dc.dat' 'c8' T '/tmp/tmpxwsyv56g/job_working_directory/000/12/outputs/dataset_42abd194-5cd7-4756-a3dc-b78969ae0c39.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8"`
dbkey	`"?"`
delimiter	`"T"`

Step 17: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpxwsyv56g/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpxwsyv56g/files/6/5/b/dataset_65b95096-3b81-43eb-8818-ba35f88022dc.dat' 'c7' T '/tmp/tmpxwsyv56g/job_working_directory/000/13/outputs/dataset_780d29c8-aa07-4970-aaed-e709a00385cc.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 18: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmpxwsyv56g/files/5/7/5/dataset_575d13cf-838f-4e2b-8984-85420dca87a1.dat' reference.fa && minimap2 -DP -k19 -w19 -m200    --min-occ-floor 100 --q-occ-frac 0.01 -m 40  -A 1 -B 19 -O 39,81 -E 3,1 -z 200      -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmpxwsyv56g/files/5/7/5/dataset_575d13cf-838f-4e2b-8984-85420dca87a1.dat' > '/tmp/tmpxwsyv56g/job_working_directory/000/14/outputs/dataset_ca99be57-d115-4214-b7a8-8f1a6ab367ce.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.061*1.01] collected minimizers
[M::mm_idx_gen::0.079*1.01] sorted minimizers
[M::main::0.080*1.01] loaded/built the index for 86 target sequence(s)
[M::mm_mapopt_update::0.082*1.01] mid_occ = 100
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 86
[M::mm_idx_stat::0.084*1.00] distinct minimizers: 156208 (93.94% are singletons); average occurrences: 1.302; average spacing: 9.990; total length: 2031175
[M::worker_pipeline::1.378*0.97] mapped 86 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -DP -k19 -w19 -m200 --min-occ-floor 100 --q-occ-frac 0.01 -m 40 -A 1 -B 19 -O 39,81 -E 3,1 -z 200 -t 1 reference.fa /tmp/tmpxwsyv56g/files/5/7/5/dataset_575d13cf-838f-4e2b-8984-85420dca87a1.dat
[M::main] Real time: 1.382 sec; CPU: 1.346 sec; Peak RSS: 0.024 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
alignment_options	`{"A": "1", "B": "19", "E": "3", "E2": "1", "O": "39", "O2": "81", "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": "200", "z2": null}`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "self-homology", "fastq_input1": {"values": [{"id": 9, "src": "hda"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "paf"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": "40", "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": "100", "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 19: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpxwsyv56g/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmpxwsyv56g/files/8/7/4/dataset_8747d498-215f-4d0a-ac84-eb8bd3d4e2b3.dat' --output='/tmp/tmpxwsyv56g/job_working_directory/000/15/outputs/dataset_05a74e63-c4cf-4f51-8cf5-9197c653a384.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"c20a66019fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpxwsyv56g/job_working_directory/000/16/configs/tmp9kud0lwz' '/tmp/tmpxwsyv56g/files/0/5/a/dataset_05a74e63-c4cf-4f51-8cf5-9197c653a384.dat' > '/tmp/tmpxwsyv56g/job_working_directory/000/16/outputs/dataset_de9e8612-cdaa-486e-ae1e-f09873278380.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66019fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmpxwsyv56g/files/d/e/9/dataset_de9e8612-cdaa-486e-ae1e-f09873278380.dat > '/tmp/tmpxwsyv56g/job_working_directory/000/17/outputs/dataset_58a7996b-b667-4294-a2d9-0a90711bd95e.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66019fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpxwsyv56g/files/d/e/9/dataset_de9e8612-cdaa-486e-ae1e-f09873278380.dat" "/tmp/tmpxwsyv56g/job_working_directory/000/18/outputs/dataset_556d594c-fb6f-4c0c-9c75-2198ca7577b0.dat" "1" "yes"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66019fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"c20a66019fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66019fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1933626", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmpxwsyv56g/job_working_directory/000/43/configs/tmpffbx9hiy' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpxwsyv56g/files/5/5/6/dataset_556d594c-fb6f-4c0c-9c75-2198ca7577b0.dat' '/tmp/tmpxwsyv56g/job_working_directory/000/43/outputs/dataset_357ba3e9-90bf-4bfe-92bc-d841e00d44ae.dat'

Exit Code:

```
0
```

Standard Output:

c3/1933626
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1933626;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 79 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66019fe611ef933e19e3a6c49587"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1933626"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 20: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpxwsyv56g/files/4/1/c/dataset_41cd89bf-b554-4489-8086-b33bd3487d9e.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmpxwsyv56g/job_working_directory/000/22/outputs/dataset_618d7673-cd3a-4870-98f3-979485553240.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 3: Assembly to purge:
- step_state: scheduled

Step 21: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 22: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpxwsyv56g/job_working_directory/000/23/configs/tmpx38n1pgw' '/tmp/tmpxwsyv56g/files/6/1/8/dataset_618d7673-cd3a-4870-98f3-979485553240.dat' > '/tmp/tmpxwsyv56g/job_working_directory/000/23/outputs/dataset_11ded666-a05b-4cfc-a775-3db61d5eaa96.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN{print \"Metric\\tAlternate\"}; {print}; "`
dbkey	`"?"`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gzip -c '/tmp/tmpxwsyv56g/files/c/f/3/dataset_cf3bb9eb-5f8c-4f05-84e6-d741c9181da0.dat' > '0.gz' && pbcstat -M 500 -f 0.0 -l 0 -p '0.gz' && mv PB.stat depth.stat && calcuts -f 0.1 -l 1 -m 16 -u 48 -d 0 depth.stat > cutoffs.tsv 2>calcuts.log && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/e9bd16ba5ebd/purge_dups/hist_plot.py' --cutoffs cutoffs.tsv --title 'Read depth histogram plot' depth.stat hist.png

Exit Code:

```
0
```

Standard Error:

Program starts
Program finished successfully

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	{"__current_case__": 2, "functions": "pbcstat", "input": {"values": [{"id": 2, "src": "hdca"}]}, "output_options": ["pbcstat_coverage", "pbcstat_wig", "depth_stats", "histogram", "calcuts_cutoff", "calcuts_log"], "pbcstat_options": {"flank": "0", "max_cov": "500", "min_map_qual": null, "min_map_ratio": "0.0", "primary_alignments": true}, "section_calcuts": {"low_depth": "1", "min_depth": "0.1", "ploidy": "-d 0", "transition": "16", "upper_depth": "48"}, "section_hist": {"title": "Read depth histogram plot", "xmax": null, "xmin": null, "ymax": null, "ymin": null}}

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gzip -c '/tmp/tmpxwsyv56g/files/c/a/9/dataset_ca99be57-d115-4214-b7a8-8f1a6ab367ce.dat' > '0.gz' && purge_dups -c '/tmp/tmpxwsyv56g/files/d/9/d/dataset_d9d89994-9d10-4f09-af46-83d348c215e8.dat' -T '/tmp/tmpxwsyv56g/files/2/5/d/dataset_25d2d504-8291-4f8d-ace8-5e7fb19d197c.dat' -f 0.8 -a 70 -b 200 -m 500 -M 20000 -l 10000 -E 15000 '0.gz' > dups.bed 2> purge_dups.log

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 0, "coverage": {"values": [{"id": 25, "src": "hda"}]}, "cutoffs": {"values": [{"id": 29, "src": "hda"}]}, "double_chain": {"__current_case__": 1, "chaining_rounds": "one"}, "functions": "purge_dups", "input": {"values": [{"id": 14, "src": "hda"}]}, "log_file": true, "max_extend": "15000", "max_gap": "20000", "min_align": "70", "min_bad": "0.8", "min_chain": "500", "min_chain_score": "10000", "min_match": "200"}`

Step 26: Remove REPEATs from BED:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

grep -P -A 0 -B 0 --no-group-separator -v -i -- 'REPEAT' '/tmp/tmpxwsyv56g/files/3/6/5/dataset_365af4db-b5d4-469b-9cf2-c63ac373cb2a.dat' > '/tmp/tmpxwsyv56g/job_working_directory/000/26/outputs/dataset_a359cfd6-a784-460c-b6ea-3a24446e0132.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`"-v"`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-P"`
url_paste	`"REPEAT"`

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

get_seqs   -e  -l 10000 -m 0.05 -g 10000 '/tmp/tmpxwsyv56g/files/a/3/5/dataset_a359cfd6-a784-460c-b6ea-3a24446e0132.dat' '/tmp/tmpxwsyv56g/files/8/1/9/dataset_819537ac-dd6b-4de0-944b-569615d46e0d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 5, "advanced_options": {"coverage": false, "end_trim": true, "haplotigs": false, "length": "10000", "min_gap": "10000", "min_ratio": "0.05", "split": false}, "bed_input": {"values": [{"id": 32, "src": "hda"}]}, "fasta_input": {"values": [{"id": 2, "src": "hda"}]}, "functions": "get_seqs"}`

Step 28: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p output_files && mkdir -p read-db.meryl && tar -zxf /tmp/tmpxwsyv56g/files/9/9/8/dataset_9989950d-b18c-41fa-9881-600b3f8d5df4.dat -C read-db.meryl --strip-components=1 && ln -s '/tmp/tmpxwsyv56g/files/6/e/8/dataset_6e812f4f-453b-450b-a7d1-0fc4d98ef944.dat' assembly_01.fasta && ln -s '/tmp/tmpxwsyv56g/files/4/1/c/dataset_41cd89bf-b554-4489-8086-b33bd3487d9e.dat' assembly_02.fasta && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta output_merqury &> /tmp/tmpxwsyv56g/job_working_directory/000/28/outputs/dataset_631c0761-0ad0-499c-893d-4be92ced6bf5.dat && mv output_merqury* output_files && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
label	`"output_merqury"`
mode	`{"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 34, "src": "hda"}]}, "assembly_02": {"values": [{"id": 5, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 3, "src": "hda"}]}, "options": "default"}`
output_add_headers	`false`
output_selector	`["qv", "plots", "stats", "log", "hist"]`

Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpxwsyv56g/files/6/e/8/dataset_6e812f4f-453b-450b-a7d1-0fc4d98ef944.dat' --out-size c   --tabular > '/tmp/tmpxwsyv56g/job_working_directory/000/29/outputs/dataset_fab5705b-da84-493f-853f-75c58f8634f0.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 30: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmpxwsyv56g/files/6/e/8/dataset_6e812f4f-453b-450b-a7d1-0fc4d98ef944.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'vertebrata_odb10'  --miniprot  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-11-11 04:59:13 ERROR:	
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-11-11 04:42:16 INFO:	***** Start a BUSCO v5.8.0 analysis, current time: 11/11/2024 04:42:16 *****
2024-11-11 04:42:16 INFO:	Configuring BUSCO with local environment
2024-11-11 04:42:16 INFO:	Running genome mode
2024-11-11 04:42:18 INFO:	Input file is /tmp/tmpxwsyv56g/files/6/e/8/dataset_6e812f4f-453b-450b-a7d1-0fc4d98ef944.dat
2024-11-11 04:42:18 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_min
2024-11-11 04:42:18 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_min
2024-11-11 04:42:18 INFO:	Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2021-02-19)
2024-11-11 04:42:18 INFO:	Running 1 job(s) on bbtools, starting at 11/11/2024 04:42:18
2024-11-11 04:42:19 INFO:	[bbtools]	1 of 1 task(s) completed
2024-11-11 04:42:19 INFO:	Running 1 job(s) on miniprot_index, starting at 11/11/2024 04:42:19
2024-11-11 04:42:20 INFO:	[miniprot_index]	1 of 1 task(s) completed
2024-11-11 04:42:20 INFO:	Running 1 job(s) on miniprot_align, starting at 11/11/2024 04:42:20
2024-11-11 04:58:16 INFO:	[miniprot_align]	1 of 1 task(s) completed
2024-11-11 04:58:22 INFO:	***** Run HMMER on gene sequences *****
2024-11-11 04:58:23 INFO:	Running 612 job(s) on hmmsearch, starting at 11/11/2024 04:58:23
2024-11-11 04:58:29 INFO:	[hmmsearch]	62 of 612 task(s) completed
2024-11-11 04:58:34 INFO:	[hmmsearch]	123 of 612 task(s) completed
2024-11-11 04:58:38 INFO:	[hmmsearch]	184 of 612 task(s) completed
2024-11-11 04:58:42 INFO:	[hmmsearch]	245 of 612 task(s) completed
2024-11-11 04:58:47 INFO:	[hmmsearch]	307 of 612 task(s) completed
2024-11-11 04:58:51 INFO:	[hmmsearch]	368 of 612 task(s) completed
2024-11-11 04:58:55 INFO:	[hmmsearch]	429 of 612 task(s) completed
2024-11-11 04:58:59 INFO:	[hmmsearch]	490 of 612 task(s) completed
2024-11-11 04:59:04 INFO:	[hmmsearch]	551 of 612 task(s) completed
2024-11-11 04:59:09 INFO:	[hmmsearch]	612 of 612 task(s) completed
2024-11-11 04:59:09 INFO:	45 exons in total
2024-11-11 04:59:09 WARNING:	1 of 35 Complete matches (2.9%) contain internal stop codons in Miniprot gene predictions
2024-11-11 04:59:09 WARNING:	BUSCO gene predictions from Miniprot have low average identity (0.47). You may want to repeat the analysis using the Metaeuk pipeline.
2024-11-11 04:59:09 INFO:	

    -------------------------------------------------------------------------------------------
    |Results from dataset vertebrata_odb10                                                     |
    -------------------------------------------------------------------------------------------
    |C:1.0%[S:1.0%,D:0.0%],F:0.1%,M:98.8%,n:3354,E:2.9%                                        |
    |35    Complete BUSCOs (C)    (of which 1 contain internal stop codons)                    |
    |34    Complete and single-copy BUSCOs (S)                                                 |
    |1    Complete and duplicated BUSCOs (D)                                                   |
    |4    Fragmented BUSCOs (F)                                                                |
    |3315    Missing BUSCOs (M)                                                                |
    |3354    Total BUSCO groups searched                                                       |
    -------------------------------------------------------------------------------------------
2024-11-11 04:59:09 INFO:	BUSCO analysis done with WARNING(s). Total running time: 1012 seconds

***** Summary of warnings: *****
2024-11-11 04:42:18 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_genome_min
2024-11-11 04:42:18 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_genome_min
2024-11-11 04:59:09 WARNING:busco.busco_tools.hmmer	1 of 35 Complete matches (2.9%) contain internal stop codons in Miniprot gene predictions
2024-11-11 04:59:09 WARNING:busco.busco_tools.hmmer	BUSCO gene predictions from Miniprot have low average identity (0.47). You may want to repeat the analysis using the Metaeuk pipeline.

2024-11-11 04:59:09 INFO:	Results written in /tmp/tmpxwsyv56g/job_working_directory/000/30/working/busco_galaxy
2024-11-11 04:59:09 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-11-11 04:59:09 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 156
drwxr-xr-x 5 1001 127  4096 Nov 11 04:42 busco_sequences
-rw-r--r-- 1 1001 127 74999 Nov 11 04:59 full_table.tsv
drwxr-xr-x 2 1001 127 20480 Nov 11 04:59 hmmer_output
drwxr-xr-x 3 1001 127  4096 Nov 11 04:58 miniprot_output
-rw-r--r-- 1 1001 127 42532 Nov 11 04:59 missing_busco_list.tsv
-rw-r--r-- 1 1001 127  2869 Nov 11 04:59 short_summary.json
-rw-r--r-- 1 1001 127  1051 Nov 11 04:59 short_summary.txt
2024-11-11 04:59:11 INFO:	****************** Start plot generation at 11/11/2024 04:59:11 ******************
2024-11-11 04:59:11 INFO:	Load data ...
2024-11-11 04:59:11 INFO:	Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully
2024-11-11 04:59:11 INFO:	Generate the R code ...
2024-11-11 04:59:11 INFO:	Run the R code ...
2024-11-11 04:59:13 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-11-11 04:59:13 INFO:	Plot generation done. Total running time: 2.10205078125 seconds
2024-11-11 04:59:13 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "use_augustus_selector": "miniprot"}}`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "missing", "image", "gff"]`

Step 4: Meryl Database:
- step_state: scheduled

Step 31: Convert purged fasta to gfa:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpxwsyv56g/files/6/e/8/dataset_6e812f4f-453b-450b-a7d1-0fc4d98ef944.dat'   -o dataset.gfa --discover-terminal-overlaps 1000 --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 79
Total scaffold length: 1884297
Average scaffold length: 23851.86
Scaffold N50: 21449
Scaffold auN: 34441.92
Scaffold L50: 28
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 79
Total contig length: 1884297
Average contig length: 23851.86
Contig N50: 21449
Contig auN: 34441.92
Contig L50: 28
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 577767:363592:365584:577354
GC content %: 38.70
# soft-masked bases: 0
# segments: 79
Total segment length: 1884297
Average segment length: 23851.86
# gaps: 0
# paths: 79
# edges: 1
Average degree: 0.01
# connected components: 1
Largest connected component length: 71428
# dead ends: 156
# disconnected components: 77
Total length disconnected components: 1812869
# separated components: 78
# bubbles: 0
# circular segments: 0
# circular paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 1, "terminal_overlaps_length": "1000", "terminal_overlaps_select": "yes"}}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 32: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmpxwsyv56g/files/6/e/8/dataset_6e812f4f-453b-450b-a7d1-0fc4d98ef944.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmpxwsyv56g/job_working_directory/000/32/outputs/dataset_c805c753-9b6e-4b52-a3d8-6842a6b6151e.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 33: merqury_QV:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
input	`{"values": [{"id": 3, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury", "which_dataset": "by_identifier"}`

Step 34: output_merqury.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 35: output_merqury.spectra-asm.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.spectra-asm.fl", "which_dataset": "by_identifier"}`

Step 36: output_merqury.assembly_01.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.assembly_01.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 37: merqury_stats:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
input	`{"values": [{"id": 5, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 38: output_merqury.assembly_02.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.assembly_02.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 39: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpxwsyv56g/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmpxwsyv56g/files/f/a/b/dataset_fab5705b-da84-493f-853f-75c58f8634f0.dat' --output='/tmp/tmpxwsyv56g/job_working_directory/000/33/outputs/dataset_81f9b2c4-e329-4db1-a0d4-6d496d6f6423.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"c20a66029fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpxwsyv56g/job_working_directory/000/34/configs/tmpdptklcvd' '/tmp/tmpxwsyv56g/files/8/1/f/dataset_81f9b2c4-e329-4db1-a0d4-6d496d6f6423.dat' > '/tmp/tmpxwsyv56g/job_working_directory/000/34/outputs/dataset_6e63ebaf-9d9f-4d31-a50d-7fe63f98deee.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66029fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmpxwsyv56g/files/6/e/6/dataset_6e63ebaf-9d9f-4d31-a50d-7fe63f98deee.dat > '/tmp/tmpxwsyv56g/job_working_directory/000/35/outputs/dataset_759760fe-28e4-48f6-958b-c505ce2fbbd5.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66029fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpxwsyv56g/files/6/e/6/dataset_6e63ebaf-9d9f-4d31-a50d-7fe63f98deee.dat" "/tmp/tmpxwsyv56g/job_working_directory/000/36/outputs/dataset_dae4522e-3e69-4f03-be7f-3a17612fc107.dat" "1" "yes"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66029fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"c20a66029fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66029fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1884297", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmpxwsyv56g/job_working_directory/000/45/configs/tmp5q9z56vr' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmpxwsyv56g/files/d/a/e/dataset_dae4522e-3e69-4f03-be7f-3a17612fc107.dat' '/tmp/tmpxwsyv56g/job_working_directory/000/45/outputs/dataset_208f53dd-1514-43e6-843e-36fc0af302d3.dat'

Exit Code:

```
0
```

Standard Output:

c3/1884297
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1884297;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 79 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66029fe611ef933e19e3a6c49587"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1884297"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 40: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmpxwsyv56g/job_working_directory/000/38/configs/tmpnd5t5k_a' '/tmp/tmpxwsyv56g/files/c/8/0/dataset_c805c753-9b6e-4b52-a3d8-6842a6b6151e.dat' > '/tmp/tmpxwsyv56g/job_working_directory/000/38/outputs/dataset_347bc4c1-9368-47c2-9bd3-9fc220ba3321.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN{print \"Metric\\tPrimary\"}; {print}; "`
dbkey	`"?"`

Step 5: Assembly to leave alone (For Merqury comparison):
- step_state: scheduled

Step 41: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Primary data:
- step_state: scheduled
Step 2: Alternate data:
- step_state: scheduled

Step 11: Size Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpxwsyv56g/job_working_directory/000/52/configs/tmpojwceedp' && Rscript '/tmp/tmpxwsyv56g/job_working_directory/000/52/configs/tmpojwceedp'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmpxwsyv56g/files/6/8/0/dataset_680c73cc-f180-40ad-9189-5be580381e28.dat', sep='\t', header=TRUE)

names(input)[2] <- "xcol"
names(input)[3] <- "ycol"

    gg_facet = NULL
    gg_factor = aes(colour=factor(factor))

        gg_line = geom_line(size=1, alpha=1, gg_factor)

        color_scale = scale_color_brewer(palette='Set1', direction='1')

    names(input)[1] <- "factor"


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmpxwsyv56g/job_working_directory/000/52/outputs/dataset_76d857a4-5415-4d11-8427-36328729a98a.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66039fe611ef933e19e3a6c49587"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"Scaffold number"`
xplot	`"2"`
ylab	`"Cumulative Size (Mb)"`
yplot	`"3"`

Step 3: Name of primary assembly:
- step_state: scheduled
Step 4: Name of alternate assembly:
- step_state: scheduled

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpxwsyv56g/files/2/0/8/dataset_208f53dd-1514-43e6-843e-36fc0af302d3.dat" "/tmp/tmpxwsyv56g/job_working_directory/000/46/outputs/dataset_723fcd8d-10ee-4a88-b19b-474ffedfc49b.dat" "Hap1" "no"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66039fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Hap1"`
iterate	`"no"`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmpxwsyv56g/files/3/5/7/dataset_357ba3e9-90bf-4bfe-92bc-d841e00d44ae.dat" "/tmp/tmpxwsyv56g/job_working_directory/000/47/outputs/dataset_5de5aed7-7d99-44f3-aea6-44bea20d66f9.dat" "Hap2" "no"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66039fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Hap2"`
iterate	`"no"`

Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpxwsyv56g/files/7/2/3/dataset_723fcd8d-10ee-4a88-b19b-474ffedfc49b.dat' >> '/tmp/tmpxwsyv56g/job_working_directory/000/48/outputs/dataset_58e2db34-2b62-44b3-96db-603c25e80593.dat' && cat '/tmp/tmpxwsyv56g/files/5/d/e/dataset_5de5aed7-7d99-44f3-aea6-44bea20d66f9.dat' >> '/tmp/tmpxwsyv56g/job_working_directory/000/48/outputs/dataset_58e2db34-2b62-44b3-96db-603c25e80593.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66039fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "inputs2": {"values": [{"id": 58, "src": "hda"}]}}]`

Step 8: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpxwsyv56g/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpxwsyv56g/files/5/8/e/dataset_58e2db34-2b62-44b3-96db-603c25e80593.dat' 'c8,c5,c6' T '/tmp/tmpxwsyv56g/job_working_directory/000/49/outputs/dataset_185710c5-ea90-443b-9b61-a00a0ff62506.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"c20a66039fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8,c5,c6"`
dbkey	`"?"`
delimiter	`"T"`

Step 9: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmpxwsyv56g/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmpxwsyv56g/files/5/8/e/dataset_58e2db34-2b62-44b3-96db-603c25e80593.dat' 'c8,c4,c7' T '/tmp/tmpxwsyv56g/job_working_directory/000/50/outputs/dataset_680c73cc-f180-40ad-9189-5be580381e28.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"c20a66039fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8,c4,c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 10: Nx Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmpxwsyv56g/job_working_directory/000/51/configs/tmp1ejda83a' && Rscript '/tmp/tmpxwsyv56g/job_working_directory/000/51/configs/tmp1ejda83a'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmpxwsyv56g/files/1/8/5/dataset_185710c5-ea90-443b-9b61-a00a0ff62506.dat', sep='\t', header=TRUE)

names(input)[2] <- "xcol"
names(input)[3] <- "ycol"

    gg_facet = NULL
    gg_factor = aes(colour=factor(factor))

        gg_line = geom_line(size=1, alpha=1, gg_factor)

        color_scale = scale_color_brewer(palette='Set1', direction='1')

    names(input)[1] <- "factor"


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmpxwsyv56g/job_working_directory/000/51/outputs/dataset_1e7a2bc4-75be-4f7b-9a85-1bb730661e97.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66039fe611ef933e19e3a6c49587"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"x"`
xplot	`"2"`
ylab	`"Nx (Mb)"`
yplot	`"3"`

Step 42: join1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmpxwsyv56g/galaxy-dev/tools/filters/join.py' '/tmp/tmpxwsyv56g/files/3/4/7/dataset_347bc4c1-9368-47c2-9bd3-9fc220ba3321.dat' '/tmp/tmpxwsyv56g/files/1/1/d/dataset_11ded666-a05b-4cfc-a775-3db61d5eaa96.dat' 1 1 '/tmp/tmpxwsyv56g/job_working_directory/000/39/outputs/dataset_0ef2678b-094e-4cf3-8054-f1968284c6f8.dat' -u -p --index_depth=3 --buffer=50000000 --fill_options_file=/tmp/tmpxwsyv56g/job_working_directory/000/39/configs/tmp4s5v2cfl

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
field1	`"1"`
field2	`"1"`
fill_empty_columns	`{"__current_case__": 1, "do_fill_empty_columns": {"__current_case__": 0, "column_fill_type": "single_fill_value", "fill_value": "."}, "fill_columns_by": "fill_unjoined_only", "fill_empty_columns_switch": "fill_empty"}`
header	`""`
partial	`"-p"`
unmatched	`"-u"`

Step 43: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cut --complement -f '3' '/tmp/tmpxwsyv56g/files/0/e/f/dataset_0ef2678b-094e-4cf3-8054-f1968284c6f8.dat' > '/tmp/tmpxwsyv56g/job_working_directory/000/40/outputs/dataset_664b079a-cc03-4d68-b7b3-db652444008d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
complement	`"--complement"`
cut_type_options	`{"__current_case__": 0, "colnames_option": {"__current_case__": 1, "header": "N", "list": ["3"]}, "cut_element": "-f", "delimiter": ""}`
dbkey	`"?"`

Step 44: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmpxwsyv56g/job_working_directory/000/41/outputs/dataset_dfbd18e3-f1ac-415d-8e00-7f5897587ec7.dat' -g     '#' 'Number of' '/tmp/tmpxwsyv56g/files/6/6/4/dataset_664b079a-cc03-4d68-b7b3-db652444008d.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"c20a66009fe611ef933e19e3a6c49587"`
chromInfo	`"/tmp/tmpxwsyv56g/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 6: Estimated genome size - Parameter File:
- step_state: scheduled
Step 7: Database for Busco Lineage:
- step_state: scheduled
Step 8: Lineage:
- step_state: scheduled
Step 9: Name of purged assembly:
- step_state: scheduled
Step 10: Name of un-altered assembly:
- step_state: scheduled

Other invocation details
- history_id
  - 216ccb6fc9760bf5
- history_state
  - ok
- invocation_id
  - 216ccb6fc9760bf5
- invocation_state
  - scheduled
- workflow_id
  - 253bfc8aa2b00984

…6b from 0.7.1 to 0.7.2

gxydevbot · 2024-12-16T04:48:00Z

There are new updates, they have been integrated to the PR, check the file diff.

github-actions · 2024-12-16T05:22:05Z

Test Results (powered by Planemo)

Test Summary

Test State	Count
Total	1
Passed	0
Error	0
Failure	1
Skipped	0

Failed Tests

❌ Purging-duplicates-one-haplotype-VGP6b.ga_0

Problems:

Output with path /tmp/tmppot405hp/Busco on data 36 short summary__e3961741-5271-41ec-a21e-cb403807192c different than expected
Expected text 'C:1.1%[S:1.1%,D:0.0%],F:0.5%,M:98.4%,n:3354' in output ('# BUSCO version is: 5.8.0 
# The lineage dataset is: vertebrata_odb10 (Creation date: 2021-02-19, number of genomes: 67, number of BUSCOs: 3354)
# Summarized benchmarking in BUSCO notation for file /tmp/tmp0rh0beq7/files/b/0/d/dataset_b0d1d06b-5b09-4a52-aa4a-4c43ee099944.dat
# BUSCO was run in mode: euk_genome_min
# Gene predictor used: miniprot

	***** Results: *****

	C:1.0%[S:1.0%,D:0.0%],F:0.1%,M:98.8%,n:3354,E:2.9%	   
	35	Complete BUSCOs (C)	(of which 1 contain internal stop codons)		   
	34	Complete and single-copy BUSCOs (S)	   
	1	Complete and duplicated BUSCOs (D)	   
	4	Fragmented BUSCOs (F)			   
	3315	Missing BUSCOs (M)			   
	3354	Total BUSCO groups searched		   

Assembly Statistics:
	79	Number of scaffolds
	79	Number of contigs
	1884297	Total length
	0.000%	Percent gaps
	21 KB	Scaffold N50
	21 KB	Contigs N50


Dependencies and versions:
	hmmsearch: 3.4
	bbtools: None
	miniprot_index: 0.13-r248
	miniprot_align: 0.13-r248
	python: sys.version_info(major=3, minor=10, micro=15, releaselevel='final', serial=0)
	busco: 5.8.0
')

Workflow invocation details

Invocation Messages

Steps

Step 1: Genomescope model parameters:
- step_state: scheduled
Step 2: Pacbio Reads Collection - Trimmed:
- step_state: scheduled

Step 11: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types float,float,float,float,float,int  --file '/tmp/tmp0rh0beq7/job_working_directory/000/7/configs/tmpne1mh8mo' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp0rh0beq7/files/d/7/0/dataset_d700b09a-47be-4ea8-a126-6cde90fb0c30.dat' '/tmp/tmp0rh0beq7/job_working_directory/000/7/outputs/dataset_9365894e-2c41-49b5-bcc7-013411d83e95.dat'

Exit Code:

```
0
```

Standard Output:

1.5*c3
3*c7
Computing 2 new columns with instructions ['1.5*c3;;', '3*c7;;']
Computed new column values for 100.00% of 1 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "1.5c3"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "3c7"}], "header_lines_select": "no"}`

Step 12: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmp0rh0beq7/files/c/4/d/dataset_c4d184d9-a9de-4fa6-9614-1ac1b1ce6ffb.dat' reference.fa && minimap2 -x asm5    --q-occ-frac 0.01       -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmp0rh0beq7/files/5/f/e/dataset_5fee2b93-c386-497b-ae86-35ff4c3a1ca4.dat' > '/tmp/tmp0rh0beq7/job_working_directory/000/8/outputs/dataset_531e89c9-7252-4946-8c54-e005b4b3e12f.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.073*0.86] collected minimizers
[M::mm_idx_gen::0.093*0.88] sorted minimizers
[M::main::0.094*0.88] loaded/built the index for 86 target sequence(s)
[M::mm_mapopt_update::0.097*0.88] mid_occ = 54
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 86
[M::mm_idx_stat::0.099*0.88] distinct minimizers: 156208 (93.94% are singletons); average occurrences: 1.302; average spacing: 9.990; total length: 2031175
[M::worker_pipeline::61.767*0.98] mapped 5789 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -x asm5 --q-occ-frac 0.01 -t 1 reference.fa /tmp/tmp0rh0beq7/files/5/f/e/dataset_5fee2b93-c386-497b-ae86-35ff4c3a1ca4.dat
[M::main] Real time: 61.771 sec; CPU: 60.270 sec; Peak RSS: 0.071 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
alignment_options	`{"A": null, "B": null, "E": null, "E2": null, "O": null, "O2": null, "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": null, "z2": null}`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "asm5", "fastq_input1": {"values": [{"id": 1, "src": "dce"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "paf"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": null, "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": null, "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 2, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 13: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

split_fa '/tmp/tmp0rh0beq7/files/c/4/d/dataset_c4d184d9-a9de-4fa6-9614-1ac1b1ce6ffb.dat' > split.fasta

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 1, "functions": "split_fa", "input": {"values": [{"id": 2, "src": "hda"}]}}`

Step 14: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp0rh0beq7/files/6/8/5/dataset_685288ee-f316-4f16-9401-0e2614681bbd.dat' --out-size c   --tabular > '/tmp/tmp0rh0beq7/job_working_directory/000/10/outputs/dataset_b632b517-baac-4a8d-a423-d8aba616323f.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 15: Estimated genome size:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"expression.json"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 16: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp0rh0beq7/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp0rh0beq7/files/9/3/6/dataset_9365894e-2c41-49b5-bcc7-013411d83e95.dat' 'c8' T '/tmp/tmp0rh0beq7/job_working_directory/000/12/outputs/dataset_29eb50f0-1992-4c7c-8f59-59812890bd69.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8"`
dbkey	`"?"`
delimiter	`"T"`

Step 17: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp0rh0beq7/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp0rh0beq7/files/9/3/6/dataset_9365894e-2c41-49b5-bcc7-013411d83e95.dat' 'c7' T '/tmp/tmp0rh0beq7/job_working_directory/000/13/outputs/dataset_717e532c-15a4-4d14-902e-9987c3caefc9.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 18: toolshed.g2.bx.psu.edu/repos/iuc/minimap2/minimap2/2.28+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

ln -f -s '/tmp/tmp0rh0beq7/files/9/f/3/dataset_9f3798a8-ae34-44c5-a5d9-3d5df6781913.dat' reference.fa && minimap2 -DP -k19 -w19 -m200    --min-occ-floor 100 --q-occ-frac 0.01 -m 40  -A 1 -B 19 -O 39,81 -E 3,1 -z 200      -t ${GALAXY_SLOTS:-4} reference.fa '/tmp/tmp0rh0beq7/files/9/f/3/dataset_9f3798a8-ae34-44c5-a5d9-3d5df6781913.dat' > '/tmp/tmp0rh0beq7/job_working_directory/000/14/outputs/dataset_82b9ddec-fe14-4c8f-9cba-2fb78d89b767.dat'

Exit Code:

```
0
```

Standard Error:

[M::mm_idx_gen::0.061*1.01] collected minimizers
[M::mm_idx_gen::0.083*0.99] sorted minimizers
[M::main::0.083*0.99] loaded/built the index for 86 target sequence(s)
[M::mm_mapopt_update::0.086*0.99] mid_occ = 100
[M::mm_idx_stat] kmer size: 19; skip: 19; is_hpc: 0; #seq: 86
[M::mm_idx_stat::0.088*0.99] distinct minimizers: 156208 (93.94% are singletons); average occurrences: 1.302; average spacing: 9.990; total length: 2031175
[M::worker_pipeline::1.278*0.98] mapped 86 sequences
[M::main] Version: 2.28-r1209
[M::main] CMD: minimap2 -DP -k19 -w19 -m200 --min-occ-floor 100 --q-occ-frac 0.01 -m 40 -A 1 -B 19 -O 39,81 -E 3,1 -z 200 -t 1 reference.fa /tmp/tmp0rh0beq7/files/9/f/3/dataset_9f3798a8-ae34-44c5-a5d9-3d5df6781913.dat
[M::main] Real time: 1.282 sec; CPU: 1.255 sec; Peak RSS: 0.028 GB

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
alignment_options	`{"A": "1", "B": "19", "E": "3", "E2": "1", "O": "39", "O2": "81", "no_end_flt": true, "s": null, "splicing": {"__current_case__": 0, "splice_mode": "preset"}, "z": "200", "z2": null}`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
fastq_input	`{"__current_case__": 0, "analysis_type_selector": "self-homology", "fastq_input1": {"values": [{"id": 9, "src": "hda"}]}, "fastq_input_selector": "single"}`
indexing_options	`{"H": false, "I": null, "k": null, "w": null}`
io_options	`{"K": null, "L": false, "Q": false, "Y": false, "c": false, "cs": null, "eqx": false, "output_format": "paf"}`
mapping_options	`{"F": null, "N": null, "X": false, "f": null, "g": null, "kmer_ocurrence_interval": {"__current_case__": 1, "interval": ""}, "m": "40", "mask_len": null, "max_chain_iter": null, "max_chain_skip": null, "min_occ_floor": "100", "n": null, "p": null, "q_occ_frac": "0.01", "r": null}`
reference_source	`{"__current_case__": 1, "ref_file": {"values": [{"id": 9, "src": "hda"}]}, "reference_source_selector": "history"}`

Step 19: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp0rh0beq7/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmp0rh0beq7/files/b/6/3/dataset_b632b517-baac-4a8d-a423-d8aba616323f.dat' --output='/tmp/tmp0rh0beq7/job_working_directory/000/15/outputs/dataset_1d05a25f-b2e8-438c-b5e8-1c296221d820.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8bb44483bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp0rh0beq7/job_working_directory/000/16/configs/tmpnwcr_oae' '/tmp/tmp0rh0beq7/files/1/d/0/dataset_1d05a25f-b2e8-438c-b5e8-1c296221d820.dat' > '/tmp/tmp0rh0beq7/job_working_directory/000/16/outputs/dataset_4beb494d-931a-4c09-9ce2-60fac4223bc8.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44483bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmp0rh0beq7/files/4/b/e/dataset_4beb494d-931a-4c09-9ce2-60fac4223bc8.dat > '/tmp/tmp0rh0beq7/job_working_directory/000/17/outputs/dataset_4b44e977-62b9-4c98-8d0c-286d743d9728.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44483bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmp0rh0beq7/files/4/b/e/dataset_4beb494d-931a-4c09-9ce2-60fac4223bc8.dat" "/tmp/tmp0rh0beq7/job_working_directory/000/18/outputs/dataset_51416c01-e1e1-451b-ab00-f044d699a76b.dat" "1" "yes"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44483bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8bb44483bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44483bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1933626", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmp0rh0beq7/job_working_directory/000/43/configs/tmpld0s4izf' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp0rh0beq7/files/5/1/4/dataset_51416c01-e1e1-451b-ab00-f044d699a76b.dat' '/tmp/tmp0rh0beq7/job_working_directory/000/43/outputs/dataset_611dae9f-5c89-48c5-b54f-41adae736378.dat'

Exit Code:

```
0
```

Standard Output:

c3/1933626
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1933626;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 79 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44483bb6a11ef899e0022484e3804"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1933626"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 20: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp0rh0beq7/files/6/8/5/dataset_685288ee-f316-4f16-9401-0e2614681bbd.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmp0rh0beq7/job_working_directory/000/22/outputs/dataset_45679b3b-bacc-4163-8f5b-df840424770b.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 3: Assembly to purge:
- step_state: scheduled

Step 21: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 22: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 23: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp0rh0beq7/job_working_directory/000/23/configs/tmpacy0hpm0' '/tmp/tmp0rh0beq7/files/4/5/6/dataset_45679b3b-bacc-4163-8f5b-df840424770b.dat' > '/tmp/tmp0rh0beq7/job_working_directory/000/23/outputs/dataset_cd8fa98d-1c37-4122-a0c4-69de387d371b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN{print \"Metric\\tAlternate\"}; {print}; "`
dbkey	`"?"`

Step 24: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gzip -c '/tmp/tmp0rh0beq7/files/5/3/1/dataset_531e89c9-7252-4946-8c54-e005b4b3e12f.dat' > '0.gz' && pbcstat -M 500 -f 0.0 -l 0 -p '0.gz' && mv PB.stat depth.stat && calcuts -f 0.1 -l 1 -m 16 -u 48 -d 0 depth.stat > cutoffs.tsv 2>calcuts.log && python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/e9bd16ba5ebd/purge_dups/hist_plot.py' --cutoffs cutoffs.tsv --title 'Read depth histogram plot' depth.stat hist.png

Exit Code:

```
0
```

Standard Error:

Program starts
Program finished successfully

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	{"__current_case__": 2, "functions": "pbcstat", "input": {"values": [{"id": 2, "src": "hdca"}]}, "output_options": ["pbcstat_coverage", "pbcstat_wig", "depth_stats", "histogram", "calcuts_cutoff", "calcuts_log"], "pbcstat_options": {"flank": "0", "max_cov": "500", "min_map_qual": null, "min_map_ratio": "0.0", "primary_alignments": true}, "section_calcuts": {"low_depth": "1", "min_depth": "0.1", "ploidy": "-d 0", "transition": "16", "upper_depth": "48"}, "section_hist": {"title": "Read depth histogram plot", "xmax": null, "xmin": null, "ymax": null, "ymin": null}}

Step 25: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gzip -c '/tmp/tmp0rh0beq7/files/8/2/b/dataset_82b9ddec-fe14-4c8f-9cba-2fb78d89b767.dat' > '0.gz' && purge_dups -c '/tmp/tmp0rh0beq7/files/d/e/e/dataset_dee27663-5de5-4ed4-add4-c574ecbf4b8a.dat' -T '/tmp/tmp0rh0beq7/files/0/a/5/dataset_0a50131c-8a54-433c-8571-d588e041cba3.dat' -f 0.8 -a 70 -b 200 -m 500 -M 20000 -l 10000 -E 15000 '0.gz' > dups.bed 2> purge_dups.log

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 0, "coverage": {"values": [{"id": 25, "src": "hda"}]}, "cutoffs": {"values": [{"id": 29, "src": "hda"}]}, "double_chain": {"__current_case__": 1, "chaining_rounds": "one"}, "functions": "purge_dups", "input": {"values": [{"id": 14, "src": "hda"}]}, "log_file": true, "max_extend": "15000", "max_gap": "20000", "min_align": "70", "min_bad": "0.8", "min_chain": "500", "min_chain_score": "10000", "min_match": "200"}`

Step 26: Remove REPEATs from BED:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

grep -P -A 0 -B 0 --no-group-separator -v -i -- 'REPEAT' '/tmp/tmp0rh0beq7/files/6/e/9/dataset_6e92e56e-d2a0-4e45-a203-2e4ea8176cb7.dat' > '/tmp/tmp0rh0beq7/job_working_directory/000/26/outputs/dataset_c6772733-03e8-420d-a64f-4de420547b99.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
case_sensitive	`"-i"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
color	`"NOCOLOR"`
dbkey	`"?"`
invert	`"-v"`
lines_after	`"0"`
lines_before	`"0"`
regex_type	`"-P"`
url_paste	`"REPEAT"`

Step 27: toolshed.g2.bx.psu.edu/repos/iuc/purge_dups/purge_dups/1.2.6+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

get_seqs   -e  -l 10000 -m 0.05 -g 10000 '/tmp/tmp0rh0beq7/files/c/6/7/dataset_c6772733-03e8-420d-a64f-4de420547b99.dat' '/tmp/tmp0rh0beq7/files/c/4/d/dataset_c4d184d9-a9de-4fa6-9614-1ac1b1ce6ffb.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
function_select	`{"__current_case__": 5, "advanced_options": {"coverage": false, "end_trim": true, "haplotigs": false, "length": "10000", "min_gap": "10000", "min_ratio": "0.05", "split": false}, "bed_input": {"values": [{"id": 32, "src": "hda"}]}, "fasta_input": {"values": [{"id": 2, "src": "hda"}]}, "functions": "get_seqs"}`

Step 28: toolshed.g2.bx.psu.edu/repos/iuc/merqury/merqury/1.3+galaxy4:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

mkdir -p output_files && mkdir -p read-db.meryl && tar -zxf /tmp/tmp0rh0beq7/files/3/c/9/dataset_3c93a445-326a-4798-8860-3c892f26ca50.dat -C read-db.meryl --strip-components=1 && ln -s '/tmp/tmp0rh0beq7/files/b/0/d/dataset_b0d1d06b-5b09-4a52-aa4a-4c43ee099944.dat' assembly_01.fasta && ln -s '/tmp/tmp0rh0beq7/files/6/8/5/dataset_685288ee-f316-4f16-9401-0e2614681bbd.dat' assembly_02.fasta && merqury.sh read-db.meryl assembly_01.fasta assembly_02.fasta output_merqury &> /tmp/tmp0rh0beq7/job_working_directory/000/28/outputs/dataset_086e553c-7fc2-4a69-b0fe-8679872131b8.dat && mv output_merqury* output_files && find . -maxdepth 1 -name 'assembly_only*' -type f -print0 | xargs -0r mv -t output_files

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
label	`"output_merqury"`
mode	`{"__current_case__": 0, "assembly_options": {"__current_case__": 1, "assembly_01": {"values": [{"id": 34, "src": "hda"}]}, "assembly_02": {"values": [{"id": 5, "src": "hda"}]}, "number_assemblies": "two"}, "meryldb_F1": {"values": [{"id": 3, "src": "hda"}]}, "options": "default"}`
output_add_headers	`false`
output_selector	`["qv", "plots", "stats", "log", "hist"]`

Step 29: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp0rh0beq7/files/b/0/d/dataset_b0d1d06b-5b09-4a52-aa4a-4c43ee099944.dat' --out-size c   --tabular > '/tmp/tmp0rh0beq7/job_working_directory/000/29/outputs/dataset_3076a531-7985-4023-b7c5-2953bde12f10.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": false, "selector": "statistics", "statistics_condition": {"__current_case__": 0, "out_size": "c", "selector": "size"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 30: toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.8.0+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

busco --in '/tmp/tmp0rh0beq7/files/b/0/d/dataset_b0d1d06b-5b09-4a52-aa4a-4c43ee099944.dat' --mode 'geno' --out busco_galaxy --cpu ${GALAXY_SLOTS:-4} --evalue 0.001 --limit 3 --contig_break 10  --offline --download_path /cvmfs/data.galaxyproject.org/byhand/busco/v5  --lineage_dataset 'vertebrata_odb10'  --miniprot  && mkdir BUSCO_summaries && ls -l busco_galaxy/run_*/ && cp busco_galaxy/short_summary.*.txt BUSCO_summaries/ && generate_plot.py -wd BUSCO_summaries -rt specific  && echo "##gff-version 3" > busco_output.gff && cat busco_galaxy/run_*/busco_sequences/*busco_sequences/*.gff >> busco_output.gff 2> /dev/null || true

Exit Code:

```
0
```

Standard Error:

2024-12-16 05:20:44 ERROR:	
Warning message:
The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.

Standard Output:

2024-12-16 05:02:48 INFO:	***** Start a BUSCO v5.8.0 analysis, current time: 12/16/2024 05:02:48 *****
2024-12-16 05:02:48 INFO:	Configuring BUSCO with local environment
2024-12-16 05:02:48 INFO:	Running genome mode
2024-12-16 05:02:51 INFO:	Input file is /tmp/tmp0rh0beq7/files/b/0/d/dataset_b0d1d06b-5b09-4a52-aa4a-4c43ee099944.dat
2024-12-16 05:02:51 WARNING:	Option evalue was provided but is not used in the selected run mode, euk_genome_min
2024-12-16 05:02:51 WARNING:	Option limit was provided but is not used in the selected run mode, euk_genome_min
2024-12-16 05:02:51 INFO:	Running BUSCO using lineage dataset vertebrata_odb10 (eukaryota, 2021-02-19)
2024-12-16 05:02:51 INFO:	Running 1 job(s) on bbtools, starting at 12/16/2024 05:02:51
2024-12-16 05:02:52 INFO:	[bbtools]	1 of 1 task(s) completed
2024-12-16 05:02:52 INFO:	Running 1 job(s) on miniprot_index, starting at 12/16/2024 05:02:52
2024-12-16 05:02:53 INFO:	[miniprot_index]	1 of 1 task(s) completed
2024-12-16 05:02:53 INFO:	Running 1 job(s) on miniprot_align, starting at 12/16/2024 05:02:53
2024-12-16 05:19:01 INFO:	[miniprot_align]	1 of 1 task(s) completed
2024-12-16 05:19:07 INFO:	***** Run HMMER on gene sequences *****
2024-12-16 05:19:08 INFO:	Running 612 job(s) on hmmsearch, starting at 12/16/2024 05:19:08
2024-12-16 05:19:20 INFO:	[hmmsearch]	62 of 612 task(s) completed
2024-12-16 05:19:29 INFO:	[hmmsearch]	123 of 612 task(s) completed
2024-12-16 05:19:37 INFO:	[hmmsearch]	184 of 612 task(s) completed
2024-12-16 05:19:46 INFO:	[hmmsearch]	245 of 612 task(s) completed
2024-12-16 05:19:55 INFO:	[hmmsearch]	307 of 612 task(s) completed
2024-12-16 05:20:04 INFO:	[hmmsearch]	368 of 612 task(s) completed
2024-12-16 05:20:13 INFO:	[hmmsearch]	429 of 612 task(s) completed
2024-12-16 05:20:21 INFO:	[hmmsearch]	490 of 612 task(s) completed
2024-12-16 05:20:30 INFO:	[hmmsearch]	551 of 612 task(s) completed
2024-12-16 05:20:40 INFO:	[hmmsearch]	612 of 612 task(s) completed
2024-12-16 05:20:40 INFO:	45 exons in total
2024-12-16 05:20:40 WARNING:	1 of 35 Complete matches (2.9%) contain internal stop codons in Miniprot gene predictions
2024-12-16 05:20:40 WARNING:	BUSCO gene predictions from Miniprot have low average identity (0.47). You may want to repeat the analysis using the Metaeuk pipeline.
2024-12-16 05:20:41 INFO:	

    -------------------------------------------------------------------------------------------
    |Results from dataset vertebrata_odb10                                                     |
    -------------------------------------------------------------------------------------------
    |C:1.0%[S:1.0%,D:0.0%],F:0.1%,M:98.8%,n:3354,E:2.9%                                        |
    |35    Complete BUSCOs (C)    (of which 1 contain internal stop codons)                    |
    |34    Complete and single-copy BUSCOs (S)                                                 |
    |1    Complete and duplicated BUSCOs (D)                                                   |
    |4    Fragmented BUSCOs (F)                                                                |
    |3315    Missing BUSCOs (M)                                                                |
    |3354    Total BUSCO groups searched                                                       |
    -------------------------------------------------------------------------------------------
2024-12-16 05:20:41 INFO:	BUSCO analysis done with WARNING(s). Total running time: 1070 seconds

***** Summary of warnings: *****
2024-12-16 05:02:51 WARNING:busco.BuscoConfig	Option evalue was provided but is not used in the selected run mode, euk_genome_min
2024-12-16 05:02:51 WARNING:busco.BuscoConfig	Option limit was provided but is not used in the selected run mode, euk_genome_min
2024-12-16 05:20:40 WARNING:busco.busco_tools.hmmer	1 of 35 Complete matches (2.9%) contain internal stop codons in Miniprot gene predictions
2024-12-16 05:20:40 WARNING:busco.busco_tools.hmmer	BUSCO gene predictions from Miniprot have low average identity (0.47). You may want to repeat the analysis using the Metaeuk pipeline.

2024-12-16 05:20:41 INFO:	Results written in /tmp/tmp0rh0beq7/job_working_directory/000/30/working/busco_galaxy
2024-12-16 05:20:41 INFO:	For assistance with interpreting the results, please consult the userguide: https://busco.ezlab.org/busco_userguide.html

2024-12-16 05:20:41 INFO:	Visit this page https://gitlab.com/ezlab/busco#how-to-cite-busco to see how to cite BUSCO
total 156
drwxr-xr-x 5 1001 118  4096 Dec 16 05:02 busco_sequences
-rw-r--r-- 1 1001 118 74999 Dec 16 05:20 full_table.tsv
drwxr-xr-x 2 1001 118 20480 Dec 16 05:20 hmmer_output
drwxr-xr-x 3 1001 118  4096 Dec 16 05:19 miniprot_output
-rw-r--r-- 1 1001 118 42532 Dec 16 05:20 missing_busco_list.tsv
-rw-r--r-- 1 1001 118  2869 Dec 16 05:20 short_summary.json
-rw-r--r-- 1 1001 118  1051 Dec 16 05:20 short_summary.txt
2024-12-16 05:20:42 INFO:	****************** Start plot generation at 12/16/2024 05:20:42 ******************
2024-12-16 05:20:42 INFO:	Load data ...
2024-12-16 05:20:42 INFO:	Loaded BUSCO_summaries/short_summary.specific.vertebrata_odb10.busco_galaxy.txt successfully
2024-12-16 05:20:42 INFO:	Generate the R code ...
2024-12-16 05:20:42 INFO:	Run the R code ...
2024-12-16 05:20:44 INFO:	
[1] "Plotting the figure ..."
[1] "Done"

2024-12-16 05:20:44 INFO:	Plot generation done. Total running time: 2.207836866378784 seconds
2024-12-16 05:20:44 INFO:	Results written in BUSCO_summaries/

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
adv	`{"contig_break": "10", "evalue": "0.001", "limit": "3"}`
busco_mode	`{"__current_case__": 0, "mode": "geno", "use_augustus": {"__current_case__": 1, "use_augustus_selector": "miniprot"}}`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
lineage	`{"__current_case__": 1, "lineage_dataset": "vertebrata_odb10", "lineage_mode": "select_lineage"}`
lineage_conditional	`{"__current_case__": 0, "cached_db": "v5", "selector": "cached"}`
outputs	`["short_summary", "missing", "image", "gff"]`

Step 4: Meryl Database:
- step_state: scheduled

Step 31: Convert purged fasta to gfa:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp0rh0beq7/files/b/0/d/dataset_b0d1d06b-5b09-4a52-aa4a-4c43ee099944.dat'   -o dataset.gfa --discover-terminal-overlaps 1000 --threads ${GALAXY_SLOTS:-8} && mv dataset* output_dataset

Exit Code:

```
0
```

Standard Output:

+++Assembly summary+++: 
# scaffolds: 79
Total scaffold length: 1884297
Average scaffold length: 23851.86
Scaffold N50: 21449
Scaffold auN: 34441.92
Scaffold L50: 28
Largest scaffold: 132632
Smallest scaffold: 11406
# contigs: 79
Total contig length: 1884297
Average contig length: 23851.86
Contig N50: 21449
Contig auN: 34441.92
Contig L50: 28
Largest contig: 132632
Smallest contig: 11406
# gaps in scaffolds: 0
Total gap length in scaffolds: 0
Average gap length in scaffolds: 0.00
Gap N50 in scaffolds: 0
Gap auN in scaffolds: 0.00
Gap L50 in scaffolds: 0
Largest gap in scaffolds: 0
Smallest gap in scaffolds: 0
Base composition (A:C:G:T): 577767:363592:365584:577354
GC content %: 38.70
# soft-masked bases: 0
# segments: 79
Total segment length: 1884297
Average segment length: 23851.86
# gaps: 0
# paths: 79
# edges: 1
Average degree: 0.01
# connected components: 1
Largest connected component length: 71428
# dead ends: 156
# disconnected components: 77
Total length disconnected components: 1812869
# separated components: 78
# bubbles: 0
# circular segments: 0
# circular paths: 0

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 0, "discover_paths": false, "homopolymer_compress": null, "output_condition": {"__current_case__": 4, "out_format": "gfa", "terminal_overlaps_condition": {"__current_case__": 1, "terminal_overlaps_length": "1000", "terminal_overlaps_select": "yes"}}, "remove_terminal_gaps": false, "selector": "manipulation", "sort": "", "swiss_army_knife": null}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 32: toolshed.g2.bx.psu.edu/repos/bgruening/gfastats/gfastats/1.3.9+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

gfastats '/tmp/tmp0rh0beq7/files/b/0/d/dataset_b0d1d06b-5b09-4a52-aa4a-4c43ee099944.dat' 2288021 --nstar-report --locale en_US.UTF-8  --tabular > '/tmp/tmp0rh0beq7/job_working_directory/000/32/outputs/dataset_297df16f-576b-4edc-874b-7a6f2952774d.dat' --threads ${GALAXY_SLOTS:-8}

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
mode_condition	`{"__current_case__": 1, "discover_paths": false, "locale": true, "selector": "statistics", "statistics_condition": {"__current_case__": 2, "expected_genomesize": "2288021", "selector": "assembly"}, "tabular": true}`
target_condition	`{"__current_case__": 0, "target_option": "false"}`

Step 33: merqury_QV:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
input	`{"values": [{"id": 3, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury", "which_dataset": "by_identifier"}`

Step 34: output_merqury.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 35: output_merqury.spectra-asm.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.spectra-asm.fl", "which_dataset": "by_identifier"}`

Step 36: output_merqury.assembly_01.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.assembly_01.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 37: merqury_stats:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
input	`{"values": [{"id": 5, "src": "hdca"}]}`
which	`{"__current_case__": 0, "which_dataset": "first"}`

Step 38: output_merqury.assembly_02.spectra-cn.fl:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Traceback:

Job Parameters:

Job parameter	Parameter value
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
input	`{"values": [{"id": 4, "src": "hdca"}]}`
which	`{"__current_case__": 1, "identifier": "output_merqury.assembly_02.spectra-cn.fl", "which_dataset": "by_identifier"}`

Step 39: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: gfa_stats:
- step_state: scheduled

Step 2: sort1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp0rh0beq7/galaxy-dev/tools/filters/sorter.py'  --input='/tmp/tmp0rh0beq7/files/3/0/7/dataset_3076a531-7985-4023-b7c5-2953bde12f10.dat' --output='/tmp/tmp0rh0beq7/job_working_directory/000/33/outputs/dataset_6eb5de4e-d3c5-4ce5-88c7-f3159035694d.dat'    --key=2,2nr   --header 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8bb44484bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
column	`"2"`
column_set	`[]`
dbkey	`"?"`
header_lines	`"0"`
order	`"DESC"`
style	`"num"`

Step 3: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp0rh0beq7/job_working_directory/000/34/configs/tmpkv5lidge' '/tmp/tmp0rh0beq7/files/6/e/b/dataset_6eb5de4e-d3c5-4ce5-88c7-f3159035694d.dat' > '/tmp/tmp0rh0beq7/job_working_directory/000/34/outputs/dataset_79a11c3f-d455-4f87-a61a-b0d2c41a39d1.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44484bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"{total += $2; $3 = total}1"`
dbkey	`"?"`

Step 4: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/1.8+galaxy0:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

datamash         absmax 3 < /tmp/tmp0rh0beq7/files/7/9/a/dataset_79a11c3f-d455-4f87-a61a-b0d2c41a39d1.dat > '/tmp/tmp0rh0beq7/job_working_directory/000/35/outputs/dataset_fa756b12-1246-42c2-ab48-7e5dbfa95787.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44484bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
grouping	`""`
header_in	`false`
header_out	`false`
ignore_case	`false`
narm	`false`
need_sort	`false`
operations	`[{"__index__": 0, "op_column": "3", "op_name": "absmax"}]`
print_full_line	`false`

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmp0rh0beq7/files/7/9/a/dataset_79a11c3f-d455-4f87-a61a-b0d2c41a39d1.dat" "/tmp/tmp0rh0beq7/job_working_directory/000/36/outputs/dataset_c04a6877-895c-4222-923c-8a5f4a6aee9e.dat" "1" "yes"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44484bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"1"`
iterate	`"yes"`

Step 6: param_value_from_file:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8bb44484bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
param_type	`"integer"`
remove_newlines	`true`

Step 7: toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

```
cd ../; python _evaluate_expression_.py
```

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44484bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
components	`[{"__index__": 0, "param_type": {"__current_case__": 0, "component_value": "c3/", "select_param_type": "text"}}, {"__index__": 1, "param_type": {"__current_case__": 1, "component_value": "1884297", "select_param_type": "integer"}}]`
dbkey	`"?"`

Step 8: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1/2.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/column_maker/aff5135563c6/column_maker/column_maker.py' --column-types str,int,int,int  --file '/tmp/tmp0rh0beq7/job_working_directory/000/45/configs/tmpnj66ay__' --fail-on-non-existent-columns --fail-on-non-computable '/tmp/tmp0rh0beq7/files/c/0/4/dataset_c04a6877-895c-4222-923c-8a5f4a6aee9e.dat' '/tmp/tmp0rh0beq7/job_working_directory/000/45/outputs/dataset_39116ddf-20c3-4642-97af-e12ad36e7772.dat'

Exit Code:

```
0
```

Standard Output:

c3/1884297
c2/1000000
c3/1000000
Computing 3 new columns with instructions ['c3/1884297;;', 'c2/1000000;;', 'c3/1000000;;']
Computed new column values for 100.00% of 79 lines written.

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44484bb6a11ef899e0022484e3804"`
avoid_scientific_notation	`false`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
error_handling	`{"auto_col_types": true, "fail_on_non_existent_columns": true, "non_computable": {"__current_case__": 0, "action": "--fail-on-non-computable"}}`
ops	`{"__current_case__": 0, "expressions": [{"__index__": 0, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1884297"}, {"__index__": 1, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c2/1000000"}, {"__index__": 2, "add_column": {"__current_case__": 0, "mode": "", "pos": ""}, "cond": "c3/1000000"}], "header_lines_select": "no"}`

Step 40: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

env -i $(which awk) --sandbox -v FS='	' -v OFS='	' --re-interval -f '/tmp/tmp0rh0beq7/job_working_directory/000/38/configs/tmp3oqv0fly' '/tmp/tmp0rh0beq7/files/2/9/7/dataset_297df16f-576b-4edc-874b-7a6f2952774d.dat' > '/tmp/tmp0rh0beq7/job_working_directory/000/38/outputs/dataset_71e23028-a6c5-44ca-88e8-befa155c3f5f.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
code	`"BEGIN{print \"Metric\\tPrimary\"}; {print}; "`
dbkey	`"?"`

Step 5: Assembly to leave alone (For Merqury comparison):
- step_state: scheduled

Step 41: Unlabelled step:

step_state: scheduled

Subworkflow Steps

Step 1: Primary data:
- step_state: scheduled
Step 2: Alternate data:
- step_state: scheduled

Step 11: Size Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp0rh0beq7/job_working_directory/000/52/configs/tmpiv6y1i5_' && Rscript '/tmp/tmp0rh0beq7/job_working_directory/000/52/configs/tmpiv6y1i5_'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmp0rh0beq7/files/4/7/9/dataset_479a165d-866e-43c5-b1bd-61a3825c725b.dat', sep='\t', header=TRUE)

names(input)[2] <- "xcol"
names(input)[3] <- "ycol"

    gg_facet = NULL
    gg_factor = aes(colour=factor(factor))

        gg_line = geom_line(size=1, alpha=1, gg_factor)

        color_scale = scale_color_brewer(palette='Set1', direction='1')

    names(input)[1] <- "factor"


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('Scaffold number') + ylab('Cumulative Size (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmp0rh0beq7/job_working_directory/000/52/outputs/dataset_a1159cd9-8ae5-4988-b528-9c3425739622.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44485bb6a11ef899e0022484e3804"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"Scaffold number"`
xplot	`"2"`
ylab	`"Cumulative Size (Mb)"`
yplot	`"3"`

Step 3: Name of primary assembly:
- step_state: scheduled
Step 4: Name of alternate assembly:
- step_state: scheduled

Step 5: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmp0rh0beq7/files/3/9/1/dataset_39116ddf-20c3-4642-97af-e12ad36e7772.dat" "/tmp/tmp0rh0beq7/job_working_directory/000/46/outputs/dataset_63dc66bc-19ec-4761-83c1-ea017b5e4c1d.dat" "Hap1" "no"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44485bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Hap1"`
iterate	`"no"`

Step 6: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue/1.0.1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl /tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/devteam/add_value/023f0a3760b3/add_value/fixedValueColumn.pl "/tmp/tmp0rh0beq7/files/6/1/1/dataset_611dae9f-5c89-48c5-b54f-41adae736378.dat" "/tmp/tmp0rh0beq7/job_working_directory/000/47/outputs/dataset_3d5054c4-1fbe-4468-81c6-f5b7b3671579.dat" "Hap2" "no"

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44485bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
exp	`"Hap2"`
iterate	`"no"`

Step 7: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp0rh0beq7/files/6/3/d/dataset_63dc66bc-19ec-4761-83c1-ea017b5e4c1d.dat' >> '/tmp/tmp0rh0beq7/job_working_directory/000/48/outputs/dataset_ff2e67b2-884c-4e57-bfdf-e61d62dd42cc.dat' && cat '/tmp/tmp0rh0beq7/files/3/d/5/dataset_3d5054c4-1fbe-4468-81c6-f5b7b3671579.dat' >> '/tmp/tmp0rh0beq7/job_working_directory/000/48/outputs/dataset_ff2e67b2-884c-4e57-bfdf-e61d62dd42cc.dat' && exit 0

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44485bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
queries	`[{"__index__": 0, "inputs2": {"values": [{"id": 58, "src": "hda"}]}}]`

Step 8: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp0rh0beq7/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp0rh0beq7/files/f/f/2/dataset_ff2e67b2-884c-4e57-bfdf-e61d62dd42cc.dat' 'c8,c5,c6' T '/tmp/tmp0rh0beq7/job_working_directory/000/49/outputs/dataset_1594fb24-64fb-4d04-b738-997deb658caa.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8bb44485bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8,c5,c6"`
dbkey	`"?"`
delimiter	`"T"`

Step 9: Cut1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/tmp0rh0beq7/galaxy-dev/tools/filters/cutWrapper.pl' '/tmp/tmp0rh0beq7/files/f/f/2/dataset_ff2e67b2-884c-4e57-bfdf-e61d62dd42cc.dat' 'c8,c4,c7' T '/tmp/tmp0rh0beq7/job_working_directory/000/50/outputs/dataset_479a165d-866e-43c5-b1bd-61a3825c725b.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8bb44485bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
columnList	`"c8,c4,c7"`
dbkey	`"?"`
delimiter	`"T"`

Step 10: Nx Plot:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cat '/tmp/tmp0rh0beq7/job_working_directory/000/51/configs/tmpw9fj_noh' && Rscript '/tmp/tmp0rh0beq7/job_working_directory/000/51/configs/tmpw9fj_noh'

Exit Code:

```
0
```

Standard Error:

Warning message:
In Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") :
  OS reports request to set locale to "en_US.UTF-8" cannot be honored
Warning message:
package ‘ggplot2’ was built under R version 4.1.3 
Warning message:
Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
ℹ Please use `linewidth` instead.

Standard Output:

        options(show.error.messages=F, error=function(){cat(geterrmessage(), file=stderr()); q("no",1,F)})

        loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
    

library(ggplot2)


        #Choose between automatically scaled x and y axis or user defined
            gg_scalex = NULL
            gg_scaley = NULL
    


            gg_theme = theme_bw()
    


            gg_legend = theme(legend.position="right")
    

input <- read.csv('/tmp/tmp0rh0beq7/files/1/5/9/dataset_1594fb24-64fb-4d04-b738-997deb658caa.dat', sep='\t', header=TRUE)

names(input)[2] <- "xcol"
names(input)[3] <- "ycol"

    gg_facet = NULL
    gg_factor = aes(colour=factor(factor))

        gg_line = geom_line(size=1, alpha=1, gg_factor)

        color_scale = scale_color_brewer(palette='Set1', direction='1')

    names(input)[1] <- "factor"


    

    gg_axistitle = theme(axis.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_axistext = theme(axis.text = element_text(color = NULL, size = NULL, face = NULL))

    gg_plottitle = theme(plot.title = element_text(color = NULL, size = NULL, face = NULL))

    gg_gridline = NULL

    gg_point = NULL

#this is the actual ggplot command to make the final plot(s)
plot_out <- ggplot(input, aes(xcol, ycol)) + gg_point + gg_line + gg_facet +
    gg_theme + gg_scalex + gg_scaley + color_scale + gg_legend + ggtitle('') + xlab('x') + ylab('Nx (Mb)')+
    gg_axistitle + gg_axistext + gg_plottitle + gg_gridline


        gg_width <- as.double('6.0')
        gg_height <- as.double('4.0')
        gg_unit <- 'in'
        gg_dpi <- as.double('300.0')
        gg_add_device <- 'none'
        output1 <- '/tmp/tmp0rh0beq7/job_working_directory/000/51/outputs/dataset_c5db6d42-9dd8-4b7f-a6fd-cced5725b3d8.dat'
        output2 <- 'XXXX'

        ggsave(filename = output1, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = "png")
        if(gg_add_device != "none"){
          ggsave(filename = output2, plot = plot_out, width = gg_width, height = gg_height, units = gg_unit, dpi = gg_dpi, device = gg_add_device)
        }

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44485bb6a11ef899e0022484e3804"`
adv	{"axis_text_customization": {"__current_case__": 0, "axis_customization": "default"}, "axis_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "factor": {"__current_case__": 1, "colororder": "1", "colors": "Set1", "factorcol": "1", "factoring": "Single"}, "gridlinecust": "default", "legend": "yes", "plot_title_customization": {"__current_case__": 0, "axis_customization": "default"}, "scaling": {"__current_case__": 0, "plot_scaling": "Automatic"}, "theme": "bw", "transform": "none", "type_conditional": {"__current_case__": 2, "type_options": "lines"}}
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
out	`{"additional_output_format": "none", "dpi_output_dim": "300.0", "height_output_dim": "4.0", "unit_output_dim": "in", "width_output_dim": "6.0"}`
title	`""`
xlab	`"x"`
xplot	`"2"`
ylab	`"Nx (Mb)"`
yplot	`"3"`

Step 42: join1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

python '/tmp/tmp0rh0beq7/galaxy-dev/tools/filters/join.py' '/tmp/tmp0rh0beq7/files/7/1/e/dataset_71e23028-a6c5-44ca-88e8-befa155c3f5f.dat' '/tmp/tmp0rh0beq7/files/c/d/8/dataset_cd8fa98d-1c37-4122-a0c4-69de387d371b.dat' 1 1 '/tmp/tmp0rh0beq7/job_working_directory/000/39/outputs/dataset_3895f9f5-72bd-4bbb-95a3-d7512cc6cd60.dat' -u -p --index_depth=3 --buffer=50000000 --fill_options_file=/tmp/tmp0rh0beq7/job_working_directory/000/39/configs/tmpqjky_puz

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"tabular"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
field1	`"1"`
field2	`"1"`
fill_empty_columns	`{"__current_case__": 1, "do_fill_empty_columns": {"__current_case__": 0, "column_fill_type": "single_fill_value", "fill_value": "."}, "fill_columns_by": "fill_unjoined_only", "fill_empty_columns_switch": "fill_empty"}`
header	`""`
partial	`"-p"`
unmatched	`"-u"`

Step 43: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy2:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

cut --complement -f '3' '/tmp/tmp0rh0beq7/files/3/8/9/dataset_3895f9f5-72bd-4bbb-95a3-d7512cc6cd60.dat' > '/tmp/tmp0rh0beq7/job_working_directory/000/40/outputs/dataset_b5a5df7a-ca6c-4587-ae18-f39d79526dad.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
complement	`"--complement"`
cut_type_options	`{"__current_case__": 0, "colnames_option": {"__current_case__": 1, "header": "N", "list": ["3"]}, "cut_element": "-f", "delimiter": ""}`
dbkey	`"?"`

Step 44: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace/9.3+galaxy1:

step_state: scheduled

Jobs

Job 1:

Job state is ok

Command Line:

perl '/tmp/shed_dir/toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/86755160afbf/text_processing/find_and_replace' -o '/tmp/tmp0rh0beq7/job_working_directory/000/41/outputs/dataset_4d4c6df3-04aa-4ab3-b18d-9c6629d3ce54.dat' -g     '#' 'Number of' '/tmp/tmp0rh0beq7/files/b/5/a/dataset_b5a5df7a-ca6c-4587-ae18-f39d79526dad.dat'

Exit Code:

```
0
```

Traceback:

Job Parameters:

Job parameter	Parameter value
__input_ext	`"input"`
__workflow_invocation_uuid__	`"8bb44482bb6a11ef899e0022484e3804"`
chromInfo	`"/tmp/tmp0rh0beq7/galaxy-dev/tool-data/shared/ucsc/chrom/?.len"`
dbkey	`"?"`
find_and_replace	`[{"__index__": 0, "caseinsensitive": false, "find_pattern": "#", "global": true, "is_regex": false, "replace_pattern": "Number of", "searchwhere": {"__current_case__": 0, "searchwhere_select": "line"}, "skip_first_line": false, "wholewords": false}]`

Step 6: Estimated genome size - Parameter File:
- step_state: scheduled
Step 7: Database for Busco Lineage:
- step_state: scheduled
Step 8: Lineage:
- step_state: scheduled
Step 9: Name of purged assembly:
- step_state: scheduled
Step 10: Name of un-altered assembly:
- step_state: scheduled

Other invocation details
- history_id
  - ab6c77265f9ba483
- history_state
  - ok
- invocation_id
  - ab6c77265f9ba483
- invocation_state
  - scheduled
- workflow_id
  - 471e3033f2ccc711

gxydevbot changed the title ~~Updating workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b from 0.7.1 to 0.7.2~~ Updating workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b from 0.7.1 to 0.7.2 Aug 22, 2024

gxydevbot force-pushed the workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b branch from b426b9c to 5829dbb Compare August 22, 2024 15:43

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Improve autoupdate planemo-autoupdate/autoupdate#36

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gxydevbot force-pushed the workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b branch from 5829dbb to 47bfb2b Compare September 23, 2024 14:02

gxydevbot force-pushed the workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b branch from 47bfb2b to 7abdfa6 Compare September 24, 2024 13:38

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Updating workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP…

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…6b from 0.7.1 to 0.7.2

gxydevbot force-pushed the workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b branch from 0b4694e to e433f38 Compare December 16, 2024 04:48

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Updating workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b from 0.7.1 to 0.7.2 #511

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Updating workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b from 0.7.1 to 0.7.2 #511

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