ERROR ~ Error executing process > 'VC_TONLY:pileup_paired_tonly (456)'

[samarth8392]

Description of the bug

Caused by:
Process VC_TONLY:pileup_paired_tonly (456) terminated with an error exit status (1)

Command executed:

gatk --java-options -Xmx48g GetPileupSummaries -I 59_NCI_NF1_Tu59_S59.bqsr.bam -V /data/CCBR_Pipeliner/Pipelines/LOGAN/resources/hg38/GATK_GRCh38.d1.vd1/somatic-hg38-af-only-gnomad.hg38.vcf.gz -L 41.bed -O 59_NCI_NF1_Tu59_S59_41.tpileup.table

Command exit status:
1

Command output:
(empty)

Command wrapper:
mkdir: cannot create directory ‘/lscratch/14741702’: Permission denied
mktemp: failed to create directory via template ‘/lscratch/14741702/nxf.XXXXXXXXXX’: No such file or directory

Work dir:
/vf/users/MPNST_EGA_analysis/Fastq_run/logan_output_51_59/work/dc/c378ce7c1b2383fce1a167b86c0373

Container:
/data/CCBR_Pipeliner/SIFS/dnousome-ccbr_logan_base-v0.3.9.img

Command used and terminal output

Relevant files

No response

System information

No response

[samarth8392]

This looks like an environment/runtime issue rather than a problem with the pipeline command itself.

The task is failing before the actual tool starts, in the Nextflow wrapper step that creates the process scratch directory. In this case, the wrapper is trying to create a temporary working directory under /lscratch/$SLURM_JOBID, but that path is not available or not writable for the job:

mkdir: cannot create directory ‘/lscratch/14741702’: Permission denied
mktemp: failed to create directory via template ‘/lscratch/14741702/nxf.XXXXXXXXXX’: No such file or directory

What this usually means:

the cluster/job did not provision /lscratch/14741702 for this job

Why this is likely not a pipeline bug:

the failure happens in the command wrapper before the main tool command runs
other jobs can succeed if /lscratch/$SLURM_JOBID is created correctly
this points to a scheduler/profile/local scratch configuration mismatch

Try rerunning the job (-resume)