[wgs-assembler-users] Again with submission issues

[Powers, J. <jp...@ex...>]

Hi all,

A few months ago I wrote in about having problems getting distributed to computing to work with our job submission system. I am happy to say we got all the kinks ironed out between qsub and our system. Unfortunately we recently upgraded to the latest checkout of pacBioToCA (as of December 11), and this seems to have broken things a bit.

I run pacBioToCA and it submits the runPBcR.sge.out.00.sh job and just quits. I looked at the log and it is calling it via qsub as follows:

qsub -A assembly -pe threads 4 -cwd -N "pBcR_asm"  -j y -o /mnt/Celera/BL21-DE3/MiSeq//tempBL21-DE3_long.clipped.corrected/runPBcR.sge.out.00 /mnt/Celera/BL21-DE3/MiSeq//tempBL21-DE3_long.clipped.corrected/runPBcR.sge.out.00.sh

I noticed that there wasn't a sync command or a hold_jid in this qsub call...is that correct? I looked at an old "out" file, and it did indeed have the sync

qsub -A assembly -sync y -pe threads 4 -cwd -N "rCA_asm" -j y -o /mnt/50X_Illum/20X_PB/temp94-3025.LongReads.20X.corrected/runCA.sge.out.00  /mnt/50X_Illum/20X_PB/temp94-3025.LongReads.20X.corrected/runCA.sge.out.00.sh

So I edited my spec file so that instead of this
sge = -A assembly

it says
sge = -A assembly -sync y

It now "looks" correct

qsub -A assembly -sync y -pe threads 4 -cwd -N "pBcR_asm"  -j y -o /mnt/Celera/BL21-DE3/Ion//tempBL21-DE3_long.clipped.corrected/runPBcR.sge.out.00 /mnt/Celera/BL21-DE3/Ion//tempBL21-DE3_long.clipped.corrected/runPBcR.sge.out.00.sh


Although now it seems to just hang.

So any ideas?

Thanks,

Jason