Missing bam files

[maxulysse]

Description of the bug

while running the Sarek 3.3.1 pre-processing step on a tumor-normal pair, the pipeline completed successfully, but it only generated the bam file for the normal sample

I tried with both 3.3.0 and 3.3.2, the same problem are still there…

Command used and terminal output

No response

Relevant files

No response

System information

No response

[Teezi]

Environment setting

ROOT="/projects/bv48/workspace-nobackup/tzy/sarek"

export SINGULARITY_CACHEDIR="$ROOT/singularity_cache"
export SINGULARITY_TMPDIR="$ROOT/tmp"
export SINGULARITY_LOCALCACHEDIR="$ROOT/tmp"

export NXF_TEMP="$ROOT/jGCT/1_preprocess/tmp"
export NXF_SINGULARITY_CACHEDIR="$ROOT/singularity_cache"
export NXF_OPTS='-Xms1g -Xmx7g'
export NXF_HOME="$ROOT/jGCT/1_preprocess/.nextflow"
export NXF_VER=23.04.3

Command-lines

nextflow run nf-core/sarek -r 3.3.2 \
-profile singularity \
--igenomes_base /projects/bv48/workspace-nobackup/tzy/sarek/references \
--genome GATK.GRCh38 \
--input samplesheet_7.csv \
--outdir /projects/bv48/workspace-nobackup/tzy/sarek/jGCT/1_preprocess/sample7 \
-config nextflow.config \
--trim_fastq true \
--save_trimmed true \
--save_mapped true \
--save_output_as_bam true \
-with-trace \
-with-timeline

[Teezi]

Terminal output

-[nf-core/sarek] Pipeline completed successfully-                                                                                                                                                                                            
Completed at: 06-Oct-2023 06:50:56
Duration    : 11h 59m 50s
CPU hours   : 1'408.0 (0.4% failed)
Succeeded   : 185
Failed      : 2

[Teezi]

Relevant files

nextflow.log
samplesheet_7.csv

[Teezi]

• Checking the preprocessing/ directory => four folders were created: fastp/, mapped/, markduplicates/, recal_table
• Checking each folder => only fastp/ folder contains both normal/ and tumor/ subfolders, others have only normal/ subfolder
• Investigating .nextflow.log => FASTP reported exit command 137 (use too much memory) but without stopping the pipeline from running