A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads
Jul-26 15:36:49.789 [TaskFinalizer-15] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCMGG_STRUCTURAL:STRUCTURAL:BAM_REPEAT_ESTIMATION_EXPANSIONHUNTER:EXPANSIONHUNTER (D2004042)'
Caused by:
Process `NFCMGG_STRUCTURAL:STRUCTURAL:BAM_REPEAT_ESTIMATION_EXPANSIONHUNTER:EXPANSIONHUNTER (D2004042)` terminated with an error exit status (2)
Command executed:
ExpansionHunter \
--sex unknown (ratio in gray area) \
--reads D2004042.cram \
--output-prefix D2004042 \
--reference GCA_000001405.15_GRCh38_full_plus_hs38d1_analysis_set.fna \
--variant-catalog variant_catalog.json
bgzip --threads 12 D2004042.vcf
bgzip --threads 12 D2004042.json
cat <<-END_VERSIONS > versions.yml
"NFCMGG_STRUCTURAL:STRUCTURAL:BAM_REPEAT_ESTIMATION_EXPANSIONHUNTER:EXPANSIONHUNTER":
expansionhunter: $( echo $(ExpansionHunter --version 2>&1) | head -1 | sed 's/^.*ExpansionHunter v//')
bgzip: $(echo $(bgzip -h 2>&1) | sed 's/^.*Version: //;s/Usage:.*//')
END_VERSIONS
Command exit status:
2
Command output:
(empty)
Command error:
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
.command.sh: line 3: syntax error near unexpected token `('
Work dir:
/kyukon/scratch/gent/vo/000/gvo00082/vsc43079/structural_WGS/NVQ_997/structural/work/72/01840b3cd2f3bfe1508aa72626f3d6
Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`
This is WGS data with very low coverage. Guess is that the sex could not be inferred because of low coverage.
Maybe an idea to include a check for the ability of sex inference. If the check is not passed, you could halt the pipeline and ask to specify in the samplesheet, but maybe a more elegant way is to issue a warning and then run both male and female calculations can be done, leaving the user the chance to assess the data and delete whatever doesn't fit. I see value in both approaches, what do you think?
Description of the bug
I came across this:
This is WGS data with very low coverage. Guess is that the
sex
could not be inferred because of low coverage.Maybe an idea to include a check for the ability of
sex
inference. If the check is not passed, you could halt the pipeline and ask to specify in the samplesheet, but maybe a more elegant way is to issue a warning and then run bothmale
andfemale
calculations can be done, leaving the user the chance to assess the data and delete whatever doesn't fit. I see value in both approaches, what do you think?Command used and terminal output
No response
Relevant files
No response
System information
No response