Open ekushele opened 1 month ago
Hi,
I'm trying to run sarek with "mutect2" for variant calling. Pipeline completes successfully, but the folder "output/variant_calling/" is empty. It seems like process MUTECT2_PAIRED run only on one interval file, the .command.sh is:
MUTECT2_PAIRED
.command.sh
#!/bin/bash -euo pipefail gatk --java-options "-Xmx29491M -XX:-UsePerfData" \ Mutect2 \ --input 1641_parp_ov.recal.cram --input FFPE_ovary.recal.cram \ --output FFPE_ovary_vs_1641_parp_ov.mutect2.chr2_16146120-32867130.vcf.gz \ --reference Homo_sapiens_assembly38.fasta \ --panel-of-normals 1000g_pon.hg38.vcf.gz \ --germline-resource af-only-gnomad.hg38.vcf.gz \ --intervals chr2_16146120-32867130.bed \ --tmp-dir . \ --f1r2-tar-gz FFPE_ovary_vs_1641_parp_ov.mutect2.chr2_16146120-32867130.f1r2.tar.gz --normal-sample OV3_1641_parp_ov cat <<-END_VERSIONS > versions.yml "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MUTECT2:MUTECT2_PAIRED": gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//') END_VERSIONS
I think it should run on all bed files combined together or run on all bed files and then combine them together...
nextflow -config config_sarek.conf run -resume -params-file new_OV3_params.yaml -profile singularity nf-core/sarek new_OV3_params.yaml file: input: new_OV3_sample_sheet.csv outdir: new_output step: mapping wes: true tools: 'mutect2,vep' genome: GATK.GRCh38 save_reference: true download_cache: true new_OV3_sample_sheet.csv: patient,sex,status,sample,lane,fastq_1,fastq_2 OV3,XX,1,FFPE_ovary,lane_1,fastq/OV3_FFPE_ovary_R1.conc.fastq.gz,fastq/OV3_FFPE_ovary_R2.conc.fastq.gz OV3,XX,0,1641_parp_ov,lane_1,fastq/1641_parp_ov_S4_R1_001.fastq.gz,fastq/1641_parp_ov_S4_R2_001.fastq.gz
No response
nextflow version: 23.04.4 nf-core/sarek: 3.4.1
Can you try again with 3.4.2?
Description of the bug
Hi,
I'm trying to run sarek with "mutect2" for variant calling. Pipeline completes successfully, but the folder "output/variant_calling/" is empty. It seems like process
MUTECT2_PAIRED
run only on one interval file, the.command.sh
is:I think it should run on all bed files combined together or run on all bed files and then combine them together...
Command used and terminal output
Relevant files
No response
System information
nextflow version: 23.04.4 nf-core/sarek: 3.4.1