Input Label Checking Fails After Hours of Processing

[DarioS]

The first line of the concise log is

Thu Sep 12 16:46:03 AEST 2019	Start pre-processing	/project/HeadNeck/DNAsequencing/mapped/LS11.bam

and the last line is

Fri Sep 13 03:21:47 AEST 2019	AssembleBreakends	/scratch/HeadNeck/DNAsequencing/assembled/SP18-144assembly.bam

The end of the detailed log has

********** The command line looks like this in the new syntax:
**********
**********    AssembleBreakends -TMP_DIR /scratch/HeadNeck/DNAsequencing -WORKING_DIR /scratch/HeadNeck/DNAsequencing -REFERENCE_SEQUENCE /project/StatBio/indexes/bwa/hg38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -WORKER_THREADS 8 -O /scratch/HeadNeck/DNAsequencing/assembled/SP18-144assembly.bam -INPUT /project/HeadNeck/DNAsequencing/mapped/LS11.bam -INPUT /project/HeadNeck/DNAsequencing/mapped/LS31.bam -INPUT_LABEL LS11\ -BLACKLIST /project/HeadNeck/problemRegions/hg38/ENCFF419RSJ.bed
**********

INPUT_LABEL must omitted or specified for every INPUT.

It's weird because that's not what I specified for --labels and the labels initially passed checking, otherwise it would not have run for hours. The beginning of the command has the form qsub -v inputString=/project/HeadNeck/DNAsequencing/mapped/LS11.bam /project/HeadNeck/DNAsequencing/mapped/LS31.bam,labelString='LS11,LS31' and the script called uses gridss.sh to run GRIDSS.

[DarioS]

I downloaded the latest GRIDSS and it still doesn't work. I did some more tests and realised that qsub is faulty and not working according to its documentation if comma separated values are provided.

If a variable=value pair contains any commas, the value must be enclosed in single or double quotes, and the variable=value pair must be enclosed in the kind of quotes not used to enclose the value.

Minimal example for others finding this in future:

qsub -P cancer -v x=Hello,"test='LS13,LS33'" /home/dstr7320/software/WholeGenome/testPass.pbs
echo "$test" > /home/dstr7320/label.txt
cat /home/dstr7320/label.txt
LS13\

The workaround is to pass labels as space-separated to qsub and then do labelString=${labelString// /,} to make them comma-separated within the PBS script before use with gridss.sh.