NCI-CGR / IlluminaSequencingAnalysis

All Illumina Sequencing Related project from Xin will be recorded in this repo
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Customized QC: checkquota error #25

Open lxwgcool opened 3 years ago

lxwgcool commented 3 years ago
  1. Get error when we use the command line "checkquota"
  2. Such commandline does not exist in all computing nodes. Therefore we cannot use this command line in the code
lxwgcool commented 3 years ago

Run the code and delete the additional jobs

Run the code

Manually change the number of parallel jobs temporarily

Use the command line below to delete the wrongly started jobs

sjobs | grep -i 'RMP' | awk '{print $2}' | while read line; do echo -e ${line}'\t'$(scontrol show jobid $line | tail -n 4 | head -n 1 | awk -F '/' '{print $8}' | awk -F '_' '{print $4}') | grep -i 'H53CWDSX2' | awk '{print $1}' | while read tmp; do scancel ${tmp}; done; done

Manually remove the related working flags

lxwgcool commented 3 years ago

Use "du -sB 1T " to replace "checkquota" command line to calculate the remaining available disk space.

lxwgcool commented 3 years ago

commandline "checkquota" only exists in "/usr/local/bin/checkquota" rather in /use/bin/. As a result only import ". /etc/.bashrc" is not enough,

lxwgcool commented 3 years ago

Add the additional logic to count the number of lite ROM used flowcells.