Re: [wgs-assembler-users] Again with submission issues

[Sergey K. <se...@um...>]

Hi,

The latest version of the pacBioToCA pipeline does not use (or require -sync y). Instead, it functions like runCA, submitting itself to the grid immediately after launch and then using the qhold option to control dependencies. It is the expected behavior for the job to quit as soon as it has submitted itself to the grid. The final output before quitting should be:
Your job 1544850 ("pBcR_asm_ccsman25") has been submitted

You can use this ID to see the job running on the grid. The file runPBcR.sge.out.00 will also record the output of the submitted job so you can track progress.

Sergey

On Jan 17, 2013, at 5:23 PM, Powers, Jason wrote:

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
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