bpipe error

[ljmorris]

Operating System

Other Linux (please specify below)

Other Linux

Rocky Linux release 8.9

Workflow Version

v1.2.1

Workflow Execution

Command line (Cluster)

Other workflow execution

No response

EPI2ME Version

No response

CLI command run

I am trying to execute he workflow using the following command:

nextflow run epi2me-labs/wf-transcriptomes --de_analysis --direct_rna --threads 4
--fastq 'wf-transcriptomes-demo/differential_expression_fastq'
--jaffal_annotation 'genCode22'
--jaffal_genome 'hg38_chr20'
--jaffal_refBase 'wf-transcriptomes-demo/chr20'
--ref_annotation 'wf-transcriptomes-demo/gencode.v22.annotation.chr20.gtf'
--ref_genome 'wf-transcriptomes-demo/hg38_chr20.fa'
--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv'
--out_dir ${OUTPUT}
-profile singularity

Workflow Execution - CLI Execution Profile

singularity

What happened?

This issue is similar to #69 which was closed. I am running the workflow with the demo dataset.

The workflow doesn't complete after 48 hours (with 128GB memory) and the problem appears to be with pipeline:gene_fusions:jaffal, e.g. in the nextflow.log:
TaskHandler[id: 14; name: pipeline:gene_fusions:jaffal (1); status: RUNNING; exit: -; error: -; workDir: /sc-projects/wf-transcriptomes/work/e8/f6d7cbff59a219ead6d5ae1b18818f]

In this directory e8/f6d7cbff59a219ead6d5ae1b18818f I get the error in .command.err:

mkdir: cannot create directory '/home/morrisl/.bpipedb': Read-only file system
ln: failed to create symbolic link '/home/morrisl/.bpipedb/jobs/102': No such file or directory

Relevant log output

mkdir: cannot create directory '/home/morrisl/.bpipedb': Read-only file system
ln: failed to create symbolic link '/home/morrisl/.bpipedb/jobs/102': No such file or directory

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]

Hi @ljmorris

Could you post the full log please?

[ljmorris]

Hi @nrhorner,

Here's the nextflow.log.
nextflow.log

[ljmorris]

Hi @nrhorner, do you have any idea what the problem might be or what I could try changing to get the workflow to run with the demo data?

[nrhorner]

Hi @ljmorris

I want to let you know that we have removed JAFFAL fusion detection from the latest release of the workflow as it was causing a few issues for us. We are currently looking into alternative solutions for fusion detection.

[ljmorris]

Hi @nrhorner,

Thanks for letting me know. I was able to run the workflow with the test data and my own data without JAFFAL. I wasn't able to run the latest version but v1.2.0 worked (nextflow run epi2me-labs/wf-transcriptomes -r v1.2.0). I think the issue was Singularity, maybe I need to update my version (I have singularity version 3.6.3 installed on a HPC cluster).

[nrhorner]

Hi @ljmorris

Have you had any luck using the latest version (1.4.0) ?