Open ljmorris opened 1 month ago
Hi @ljmorris
Could you post the full log please?
Hi @nrhorner,
Here's the nextflow.log. nextflow.log
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?
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.
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).
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
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