Open maxulysse opened 9 months ago
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
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
Relevant files
preprocessing/
directory => four folders were created: fastp/
, mapped/
, markduplicates/
, recal_table
fastp/
folder contains both normal/
and tumor/
subfolders, others have only normal/
subfolder.nextflow.log
=> FASTP
reported exit command 137 (use too much memory) but without stopping the pipeline from running
Description of the bug
Command used and terminal output
No response
Relevant files
No response
System information
No response