Same case_id and sample causes crash in SVDB_MERGE_ME #720
Description
Description of the bug
The input and output file names are the same if sample and case_id are the same in the sample sheet.
Pipeline version 2.6.0.
Execution cancelled -- Finishing pending tasks before exit
ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (NA12878)'
Caused by:
Missing output file(s) `*.{vcf,vcf.gz,bcf,bcf.gz}` expected by process `NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME (NA12878)` (note: input files are not included in the default matching set)
Command executed:
svdb \
--merge \
--bnd_distance 150 --overlap 0.5 \
\
--vcf NA12878_mobile_elements.vcf.gz |\
bcftools view \
\
--threads 1 \
--output NA12878_mobile_elements.vcf.gz
cat <<-END_VERSIONS > versions.yml
"NFCORE_RAREDISEASE:RAREDISEASE:CALL_MOBILE_ELEMENTS:SVDB_MERGE_ME":
svdb: $( echo $(svdb) | head -1 | sed 's/usage: SVDB-\([0-9]\.[0-9]\.[0-9]\).*/\1/' )
bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
END_VERSIONS
Command exit status:
0
Command output:
(empty)
Command error:
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
Work dir:
/data/ephemeral/na12878_med_pipeline/work/59/fd1de1eadd69aeadbeba05bec35bdc
Container:
/data/nobackup/nsc/raredisease-configs/singularity/depot.galaxyproject.org-singularity-mulled-v2-375a758a4ca8c128fb9d38047a68a9f4322d2acd-b3615e06ef17566f2988a215ce9e10808c1d08bf-0.img
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`
-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '.nextflow.log' file for details
Join mismatch for the following entries: key=[id:NA12878, sample:NA12878, sex:2, phenotype:2, paternal:0, maternal:0, case_id:NA12878, num_lanes:1, read_group:'@RG\tID:NA12878\tPL:illumina\tSM:NA12878', single_end:false] values=
Join mismatch for the following entries: key=[id:NA12878, sample:NA12878, sex:2, phenotype:2, paternal:0, maternal:0, case_id:NA12878, num_lanes:1, read_group:'@RG\tID:NA12878\tPL:illumina\tSM:NA12878', single_end:false] values=
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '.nextflow.log' file for details
-[nf-core/raredisease] Pipeline completed with errors-
WARN: Killing running tasks (3)
Command used and terminal output
Relevant files
No response
System information
No response