This is a test version of Biostars. For the public version, visit https://www.biostars.org.
STARindex PBS job quits shortly after queuing
#!/bin/bash

#PBS -m e
#PBS -M ####@###.edu
#PBS -k oe
#PBS -l nodes=1:ppn=2
#PBS -l vmem=64GB
#PBS -l walltime=24:00:00
#PBS -n starIndex


# Load modules

module load star/2.7.3a

STAR --runThreadN 23 --runMode genomeGenerate --genomeDir /home/u****/D***/RNA --genomeFastaFiles /home/u*****/D***/RNA/GRCh38.p13_genomic.fna --sjdbGTFfile /home/u*****/D****/RNA/GRCh38.p13_genomic.gtf

ERROR Report

   'PBS Job Id: 2276417.radiation.dldcc.bcm.edu
    Job Name:   test1219.pbs
    Exec host:  compute-1-3/2
    An error has occurred processing your job, see below.
    Post job file processing error; job 2276417.radiation.dldcc.bcm.edu on host compute-1-3/2

    Unable to copy file /var/spool/torque/spool/2276417.radiation.dldcc.bcm.edu.OU to /home/test1219.pbs.o2276417
    *** error from copy
    /bin/cp: cannot create regular file `/home/test1219.pbs.o2276417': Permission denied
    *** end error output
    Output retained on that host in: /var/spool/torque/undelivered/2276417.radiation.dldcc.bcm.edu.OU

    Unable to copy file /var/spool/torque/spool/2276417.radiation.dldcc.bcm.edu.ER to /home/test1219.pbs.e2276417
    *** error from copy
    /bin/cp: cannot create regular file `/home/test1219.pbs.e2276417': Permission denied
    *** end error output
    Output retained on that host in: /var/spool/torque/undelivered/2276417.radiation.dldcc.bcm.edu.ER'

The above script submits fine and is visible in qstat but then quits shortly after submitting, the actual STAR command works in interactive, so it seems to be something with the job parameters. If someone can tell me if I am missing something or if anyone could offer any advice it would be greatly appreciated.

rna-seq
• 108 views • link
written by dk0319 • dk0319

Remove the 

#PBS -k oe

and add

#PBS -e ${PBS_JOBNAME}.${PBS_JOBID%%.*}.pbserr
#PBS -o ${PBS_JOBNAME}.${PBS_JOBID%%.*}.pbsout

Maybe the -k is causing the problem. In any case, email cluster support - a few nodes of DLDCC might be down. You may not get an answer until Monday though.

• 0 views • link
written by Ram Ram

Thank you for the suggestion. Would you mind telling me how to read those commands, i.e. are they generic? or do I need to customize them to meet my specific job? Thanks

• 0 views • link
written by dk0319 • dk0319

You don't need to customize them - they will use your job name and job identifier to create unique output and error files each time you run a job. This way, your output/error files are preserved.

I've literally copy-pasted from my DLDCC job template (I'm at BCM as well), so it should work as-is.

• 0 views • link
written by Ram Ram

Thanks for the clarification. Unfortunately that did not help. I will take your advice and contact cluster support

• 0 views • link
written by dk0319 • dk0319

You-ve cross-posted on Bioinfo SE: https://bioinformatics.stackexchange.com/questions/15096/starindex-pbs-job-quits-shortly-after-queuing

I understand you're desperate for an answer, but remember that shotgun-posting (creating multiple threads on different forums asking the same question) is bad etiquette and it annoys users in both forums. Given that we have a wide overlap between these forums, doing this will turn people off against helping you on either site.

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written by Ram Ram

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