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Mageck MLE Failes with non trival design matrix. #211

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andrewholding opened this issue Oct 16, 2024 · 3 comments
Open

Mageck MLE Failes with non trival design matrix. #211

andrewholding opened this issue Oct 16, 2024 · 3 comments
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bug Something isn't working

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@andrewholding
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Description of the bug

Using the any design matrix with more then 3 samples there pipeline exists from Magick MLE with the following error.

Command error:
INFO @ Wed, 16 Oct 2024 15:53:18: Parameters: /usr/local/bin/mageck mle --threads 6 -k count_table.count.txt -n designmatrix-anh004 -d designmatrix-anh004.txt
INFO @ Wed, 16 Oct 2024 15:53:23: Cannot parse design matrix as a string; try to parse it as a file name ...
INFO @ Wed, 16 Oct 2024 15:53:23: Design matrix:
INFO @ Wed, 16 Oct 2024 15:53:23: [[1. 1. 0.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 0.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 0. 0.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 0. 0.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 1.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 1.]]
INFO @ Wed, 16 Oct 2024 15:53:23: Beta labels:baseline,common,hypoxiaVsNormoxia
INFO @ Wed, 16 Oct 2024 15:53:23: Included samples:day0-1,day0-2,control1,control2,hypoxia1,hypoxia2
INFO @ Wed, 16 Oct 2024 15:53:23: Loaded samples:day0-1;day0-2;control1;control2;hypoxia1;hypoxia2
INFO @ Wed, 16 Oct 2024 15:53:23: Sample index: 4;5;2;3;0;1
INFO @ Wed, 16 Oct 2024 15:53:23: Loaded 182 genes.
Error loading line 218
Error loading line 521
Error loading line 907
Traceback (most recent call last):
File "/usr/local/bin/mageck", line 66, in
main();
File "/usr/local/bin/mageck", line 43, in main
args=crisprseq_parseargs();
File "/usr/local/lib/python3.9/site-packages/mageck/argsParser.py", line 258, in crisprseq_parseargs
mageckmle_main(parsedargs=args); # ignoring the script path, and the sub command
File "/usr/local/lib/python3.9/site-packages/mageck/mlemageck.py", line 74, in mageckmle_main
allgenedict=read_gene_from_file(args.count_table,includesamples=args.include_samples)
File "/usr/local/lib/python3.9/site-packages/mageck/mleinstanceio.py", line 84, in read_gene_from_file
ginst.nb_count=np.matrix(ginst.nb_count)
File "/usr/local/lib/python3.9/site-packages/numpy/matrixlib/defmatrix.py", line 145, in new
arr = N.array(data, dtype=dtype, copy=copy)
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (6,) + inhomogeneous part.

The follow inputs were used:

Sample sheet
sample,fastq_1,fastq_2,condition
RM-231Hxn1,./seqdata231/RM-231Hxn1_R1_001.fastq.gz,,hypoxia1
RM-231Hxn2,./seqdata231/RM-231Hxn2_R1_001.fastq.gz,,hypoxia2
RM-231Nxn1,./seqdata231/RM-231Nxn1_R1_001.fastq.gz,,control1
RM-231Nxn2,./seqdata231/RM-231Nxn2_R1_001.fastq.gz,,control2
RM-231T0n1,./seqdata231/RM-231T0n1_R1_001.fastq.gz,,day0-1
RM-231T0n2,./seqdata231/RM-231T0n2_R1_001.fastq.gz,,day0-2

Guide library (head):
id target transcript gene symbol
1 ACCAGGGGAGCCAAGTGGA ATP1A1
2 GAAGGAGCCCCGAACCCGG ATP1A1
3 ggcggacacgtggcaacag ATP1A1
4 GAGGGAGCGCAGTAACGGG ATP1A1
5 acagcggtagcagcccggg ATP1A1
6 CCAGCCCGTCTGGGACAGT ATP1A2
7 GGGCTGTGGGTCTAACTGT ATP1A2
8 AGGGAAGGACTAGAGATGT ATP1A2
9 AGCCCACACCAGCCCGTCT ATP1A2

Design Matrix:
Samples baseline common hypoxiaVsNormoxia
day0-1 1 1 0
day0-2 1 1 0
control1 1 0 0
control2 1 0 0
hypoxia1 1 1 1
hypoxia2 1 1 1

Command used and terminal output

nextflow run nf-core/crisprseq --analysis screening --input $sampleSheet -profile apptainer
--library $guideLibrary --outdir $output
--mle_design_matrix $designMatrix
-w work-combined-day0

Relevant files

N E X T F L O W ~ version 23.10.0
Launching https://github.com/nf-core/crisprseq [loving_planck] DSL2 - revision: b2c583a [master]
WARN: Nextflow self-contained distribution allows only core plugins -- User config plugins will be ignored: [email protected]
WARN: Access to undefined parameter reference_fasta -- Initialise it to a default value eg. params.reference_fasta = some_value
WARN: Access to undefined parameter monochromeLogs -- Initialise it to a default value eg. params.monochromeLogs = some_value

                                    ,--./,-.
    ___     __   __   __   ___     /,-._.--~'

|\ | |__ __ / / \ |__) |__ } { | \| | \__, \__/ | \ |___ \-.,--, .,._,'
nf-core/crisprseq v2.2.1-gb2c583a

Core Nextflow options
revision : master
runName : loving_planck
containerEngine : apptainer
launchDir : /mnt/scratch/projects/biol-student-2023/NextFlowPipelineRM
workDir : /mnt/scratch/projects/biol-student-2023/NextFlowPipelineRM/work-combined-day0
projectDir : /users/anh524/.nextflow/assets/nf-core/crisprseq
userName : anh524
profile : apptainer
configFiles :

Input/output options
input : settings/samplesheet-anh003.csv
outdir : anh231-mle-day0
analysis : screening

Screening parameters
library : settings/guide_library-anh001.tsv
mle_design_matrix: settings/designmatrix-anh004.txt

!! Only displaying parameters that differ from the pipeline defaults !!

If you use nf-core/crisprseq for your analysis please cite:

executor > local (8)
[93/ee583d] process > NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:FASTQC (RM-231T0n2) [100%] 6 of 6 ✔
[99/4c6443] process > NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_COUNT (hypoxia1,hypoxia2,control1,control2,day0-1,day0-2) [100%] 1 of 1 ✔
[20/ebfc47] process > NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_MLE_MATRIX (designmatrix-anh004) [100%] 1 of 1, failed: 1 ✘
[- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE -
[- ] process > NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/crisprseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_MLE_MATRIX (designmatrix-anh004)'

Caused by:
Process NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_MLE_MATRIX (designmatrix-anh004) terminated with an error exit status (1)

Command executed:

mageck
mle

--threads 6
-k count_table.count.txt
-n designmatrix-anh004
-d designmatrix-anh004.txt

cat <<-END_VERSIONS > versions.yml
"NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_MLE_MATRIX":
mageck: $(mageck -v)
END_VERSIONS

Command exit status:
1

Command output:
Error loading line 218
Error loading line 521
Error loading line 907

Command error:
INFO @ Wed, 16 Oct 2024 15:53:18: Parameters: /usr/local/bin/mageck mle --threads 6 -k count_table.count.txt -n designmatrix-anh004 -d designmatrix-anh004.txt
INFO @ Wed, 16 Oct 2024 15:53:23: Cannot parse design matrix as a string; try to parse it as a file name ...
INFO @ Wed, 16 Oct 2024 15:53:23: Design matrix:
INFO @ Wed, 16 Oct 2024 15:53:23: [[1. 1. 0.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 0.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 0. 0.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 0. 0.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 1.]
INFO @ Wed, 16 Oct 2024 15:53:23: [1. 1. 1.]]
INFO @ Wed, 16 Oct 2024 15:53:23: Beta labels:baseline,common,hypoxiaVsNormoxia
INFO @ Wed, 16 Oct 2024 15:53:23: Included samples:day0-1,day0-2,control1,control2,hypoxia1,hypoxia2
INFO @ Wed, 16 Oct 2024 15:53:23: Loaded samples:day0-1;day0-2;control1;control2;hypoxia1;hypoxia2
INFO @ Wed, 16 Oct 2024 15:53:23: Sample index: 4;5;2;3;0;1
INFO @ Wed, 16 Oct 2024 15:53:23: Loaded 182 genes.
Error loading line 218
Error loading line 521
Error loading line 907
Traceback (most recent call last):
File "/usr/local/bin/mageck", line 66, in
main();
File "/usr/local/bin/mageck", line 43, in main
args=crisprseq_parseargs();
File "/usr/local/lib/python3.9/site-packages/mageck/argsParser.py", line 258, in crisprseq_parseargs
mageckmle_main(parsedargs=args); # ignoring the script path, and the sub command
File "/usr/local/lib/python3.9/site-packages/mageck/mlemageck.py", line 74, in mageckmle_main
allgenedict=read_gene_from_file(args.count_table,includesamples=args.include_samples)
File "/usr/local/lib/python3.9/site-packages/mageck/mleinstanceio.py", line 84, in read_gene_from_file
ginst.nb_count=np.matrix(ginst.nb_count)
File "/usr/local/lib/python3.9/site-packages/numpy/matrixlib/defmatrix.py", line 145, in new
arr = N.array(data, dtype=dtype, copy=copy)
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (6,) + inhomogeneous part.

Work dir:
/mnt/scratch/projects/biol-student-2023/NextFlowPipelineRM/work-combined-day0/20/ebfc47d70920ccc3aa3c2ea08f6da1

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details

System information

No response
@andrewholding andrewholding added the bug Something isn't working label Oct 16, 2024
@LaurenceKuhl
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Hi Andrew,

this seems to be coming more from MAGeCK MLE than from the pipeline, could you by any chance double check that everything is tab separated?

@andrewholding
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Have double checked, it is tab seperated. This has been picked up by @medmaca in the bioinformics core at York.

@LaurenceKuhl
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Hi @medmaca,

is there anyway i could have a subset of the count table to try to run it outside of the pipeline? I'd like to double check on my side and try a few things out! Thanks a bunch :)

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@andrewholding @LaurenceKuhl