Hello, I am facing same issues in running manta. Specifically, I am getting this error:

`ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (mgpf-ib001-10-000-000)'
Caused by:
 Process NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE (mgpf-ib001-10-000-000) terminated with an error exit status (1)
Command executed:
configManta.py 
 --bam mgpf-ib001-10-000-000.recal.bam 
 
 --reference Homo_sapiens_assembly38.fasta 
 --runDir manta 
 --callRegions wgs_calling_regions_noseconds.hg38.bed.gz \
python manta/runWorkflow.py -m local -j 30
mv manta/results/variants/candidateSmallIndels.vcf.gz 
 mgpf-ib001-10-000-000.manta.candidate_small_indels.vcf.gz
 mv manta/results/variants/candidateSmallIndels.vcf.gz.tbi 
 mgpf-ib001-10-000-000.manta.candidate_small_indels.vcf.gz.tbi
 mv manta/results/variants/candidateSV.vcf.gz 
 mgpf-ib001-10-000-000.manta.candidate_sv.vcf.gz
 mv manta/results/variants/candidateSV.vcf.gz.tbi 
 mgpf-ib001-10-000-000.manta.candidate_sv.vcf.gz.tbi
 mv manta/results/variants/diploidSV.vcf.gz 
 mgpf-ib001-10-000-000.manta.diploid_sv.vcf.gz
 mv manta/results/variants/diploidSV.vcf.gz.tbi 
 mgpf-ib001-10-000-000.manta.diploid_sv.vcf.gz.tbi
cat <<-END_VERSIONS > versions.yml
 "NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_GERMLINE_MANTA:MANTA_GERMLINE":
 manta: $( configManta.py --version )
 END_VERSIONS
Command exit status:
 1`

I am also running other modules (tiddit, strelka, mutect2) and they did not report any error. I also tried to give as input the fastq to manta instead of BAM files, but I got the same error. Did anyone experienced this same issue? Thanks for your help!

Can you look in the work folder to see if you can get more information about the error itself?

You can find the work directory of a specific (failing) process in the

exection_report_*.html

or the

.nextflow.log

(in this case, search for

MANTA_GERMLINE (mgpf-ib001-10-000-000)

). In that directory, have a look at any messages in the

.command.{out,err,log}

files.