Check script '.....nextflow/assets/epi2me-labs/wf-transcriptomes/main.nf' at line: 735 or see '.nextflow.log' file for more details

[sejmodha]

Operating System

Ubuntu 22.04

Other Linux

No response

Workflow Version

v1.5.0

Workflow Execution

Command line (Local)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-transcriptomes --fastq input_fastq/ --ref_genome reference/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz --transcriptome_source precomputed --ref_transcriptome reference/Homo_sapiens.GRCh38.cdna.all.fa.gz --ref_annotation reference/Homo_sapiens.GRCh38.113.gff3.gz --threads 16 --pychopper_op --cdna_kit SQK-PCB114 -profile standard --sample_sheet sample_sheet.csv --de_analysis -bg -r v1.5.0

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

Having switched from v1.4.0 to v1.5.0, I am getting following error.

--------------------------------------------------------------------------------
This is epi2me-labs/wf-transcriptomes v1.5.0-gb3fbb11.
--------------------------------------------------------------------------------
Reference Transcriptome provided will be used for differential expression.
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Access to 'merge_gff_bundles.out' is undefined since the process 'merge_gff_bundles' has not been invoked before accessing the output attribute

 -- Check script '/home/sejal.modha/.nextflow/assets/epi2me-labs/wf-transcriptomes/main.nf' at line: 735 or see '.nextflow.log' file for more details

Command:

nextflow run epi2me-labs/wf-transcriptomes --fastq input_fastq/ --ref_genome reference/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz --transcriptome_source precomputed --ref_transcriptome reference/Homo_sapiens.GRCh38.cdna.all.fa.gz --ref_annotation reference/Homo_sapiens.GRCh38.113.gff3.gz --threads 16  --pychopper_op --cdna_kit SQK-PCB114 -profile standard --sample_sheet sample_sheet.csv  --de_analysis -bg -r v1.5.0

I am running this workflow on an Ubuntu machine with 16 CPUs and 64 GB RAM. I have tried using v1.4.0 which does not throw the same error but runs out of memory when running makeReport process. I have tried to specify memory.config or local.config and tried to limit the RAM to 16GB as mentioned in a number of different issues/posts here but that does not fix the issue. Hence, I decided to run the most recent version of the wf assuming that memory issue might be fixed in the newer version. However, the newer version is throwing a new error!

Thanks for your help in advance.

Relevant log output

--------------------------------------------------------------------------------
This is epi2me-labs/wf-transcriptomes v1.5.0-gb3fbb11.
--------------------------------------------------------------------------------
Reference Transcriptome provided will be used for differential expression.
Searching input for [.fastq, .fastq.gz, .fq, .fq.gz] files.
Access to 'merge_gff_bundles.out' is undefined since the process 'merge_gff_bundles' has not been invoked before accessing the output attribute

 -- Check script '/home/sejal.modha/.nextflow/assets/epi2me-labs/wf-transcriptomes/main.nf' at line: 735 or see '.nextflow.log' file for more details
Command:

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

no

Other demo data information

No response

[nrhorner]

Thanks for opening the bug report @sejmodha.

I've managed to recreate your issue. It is indeed a bug that was introduced in v1.5.0 when precomputed transcriptome source is used. I will get a fix out ASAP and get back to you.

[nrhorner]

@sejmodha

Could you test out the latest version (1.6.0) and see if that fixes your issue please?

[sejmodha]

Hi @nrhorner

Apologies for a late response, I have not had a chance to test this - feel free to close this if you are sure that the error has been resolved though.

Thank you
Sej