Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Input Label Checking Fails After Hours of Processing #245

Closed
DarioS opened this issue Sep 14, 2019 · 1 comment
Closed

Input Label Checking Fails After Hours of Processing #245

DarioS opened this issue Sep 14, 2019 · 1 comment

Comments

@DarioS
Copy link

DarioS commented Sep 14, 2019

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.

d-cameron pushed a commit that referenced this issue Sep 17, 2019
…guments that whitespaces would cause the driver script to break on
@DarioS
Copy link
Author

DarioS commented Sep 19, 2019

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.

@DarioS DarioS closed this as completed Sep 19, 2019
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant