Closed ChristopherRichie closed 8 months ago
Hi @ChristopherRichie!
I was able to reproduce the error and the bug will be fixed in the next release. A workaround for the meantime would be to run with --annotation true
as this will avoid the name collision.
thanks, i will give it a try!
This has been fixed in the most recent release (v0.5.1). Please reopen this issue if the problem persists (when running with with --annotation false
).
Thanks I will give it another try!
From: Julian Libiseller-Egger @.> Sent: Wednesday, October 18, 2023 12:44 PM To: epi2me-labs/wf-somatic-variation @.> Cc: Richie, Christopher (NIH/NIDA) [E] @.>; Mention @.> Subject: [EXTERNAL] Re: [epi2me-labs/wf-somatic-variation] There are multiple input files for each of the following file names: OPTIONAL_FILE (Issue #12)
This has been fixed in the most recent release (v0.5.1). Please reopen this issue if the problem persists (when running with with --annotation false).
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Operating System
Ubuntu 22.04
Other Linux
No response
Workflow Version
v0.5.0
Workflow Execution
Command line
EPI2ME Version
No response
CLI command run
normal='//data/chrisr/older_data_for_backup/CR2839/LVF910_pool/09-29-23_clean_copy/BC06_wf-align/fastq.sorted.aligned.bam' tumor='//data/chrisr/older_data_for_backup/CR2839/LVF910_pool/09-29-23_clean_copy/BC05_wf-align/fastq.sorted.aligned.bam' basecaller_config="dna_r9.4.1_e8_sup@v3.3"
nextflow run epi2me-labs/wf-somatic-variation \ -c //data/chrisr/nextflow.config.Qi \ -profile biowulflocal \ --snv false \ --sv true \ --sample_name 'SV_mysample' \ --ref '//data/chrisr/UCSC_Rn6/genome.fa' \ --bam_normal $normal \ --bam_tumor $tumor \ --basecaller_cfg $basecaller_config \ --normal_min_coverage 0 \ --tumor_min_coverage 0 \ --classify_insert false \ --annotation false
Workflow Execution - CLI Execution Profile
custom
What happened?
I am trying to run wf-somatic-variation, using the rat genome, and two samples that have been aligned with wf-align
when I run for SNVs, the wf completes with valid outputs.
when I run with SVs, I get this error:
ERROR ~ Error executing process > 'somatic_sv:report (1)'
Caused by: Process
somatic_sv:report
input file name collision -- There are multiple input files for each of the following file names: OPTIONAL_FILE Tip: you can replicate the issue by changing to the process work dir and entering the commandbash .command.run
-- Check '.nextflow.log' file for details
I see "optional_file" in various places around the wf's github, but I do not understand if this is a bug or if I have set up the wrong command.
Relevant log output
Application activity log entry
No response