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

workflow/main.nf

@@ -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