Commit ea67847f authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

40-set.ulimit-u.for.256v1.node.thread.error

parent fa4b88e3
Pipeline #7320 failed with stages
in 4 minutes and 9 seconds
......@@ -65,6 +65,7 @@ process checkDesignFile {
script:
"""
hostname
ulimit -u 16384
ulimit -a
noSpaceDesign=\$(echo "${designLocation}" | tr -d ' ')
if [[ "\${noSpaceDesign}" != "${designLocation}" ]]; then
......@@ -96,6 +97,7 @@ process untarBCL {
script:
"""
hostname
ulimit -u 16384
ulimit -a
bash untarBCL.sh -t ${tar}
bash versions_pigz.sh > version_pigz.txt
......@@ -126,7 +128,8 @@ process mkfastq {
script:
"""
hostname
ulimit -a
ulimit -u 16384
ulimit -a
cellranger mkfastq --id=mkfastq_${bcl.simpleName} --run=${bcl} --csv=${design} --use-bases-mask=Y28n*,I8n*,n*,Y* --ignore-dual-index
mkdir fq
mkdir "fq/${bcl.simpleName}"
......@@ -155,6 +158,9 @@ if (bclCount.value == 1) {
script:
"""
hostname
ulimit -u 16384
ulimit -a
bash countDesign.sh
"""
......@@ -180,6 +186,7 @@ process fastqc {
script:
"""
hostname
ulimit -u 16384
ulimit -a
find *.fastq.gz -exec mv {} ${bcl}.{} \\;
bash fastqc.sh
......@@ -211,6 +218,7 @@ process versions {
script:
"""
hostname
ulimit -u 16384
ulimit -a
python3 generate_versions.py -f version_*.txt -o versions
python3 generate_references.py -r ${references} -o references
......@@ -236,6 +244,7 @@ process multiqc {
script:
"""
hostname
ulimit -u 16384
ulimit -a
export LC_ALL=C.UTF-8
export LANG=C.UTF-8
......
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