#265 pacBioToCA gives error for runPartition.sh

consensus
closed
nobody
None
5
2014-12-02
2014-02-03
Tae-Hyuk Ahn
No

Hi,

pacBioToCA gives errors for running runPartition.sh step.

The last line of the error file is
Failed to run correction job 1. Remove $WORKDIR/runPartition.sh to try again.

The step seemed to be started correctly as
$WORKDIR/runPartition.sh 1
$WORKDIR/runPartition.sh 2
...

But suddenly gave errors as this
$WORKDIR/runPartition.sh 16
$WORKDIR/runPartition.sh: line 73: 46000 Killed $bin/outputLayout -e 0.25 -M 0 -o $WORKDIR/asm -p $jobid -l 500 -G $WORKDIR/asm.gkpStore > $WORKDIR/$jobid.lay.err 2>&1

Please let me get your comments for this. If you need further info for running this job, I will provide it.

Thanks,

Ted

Discussion

  • Sergey Koren
    Sergey Koren
    2014-04-04

    Hi,

    This looks like the job was killed by your system. Are any errors reported in *.lay.err? One other suggestion, for CA 8.1, you can use a faster consensus module which may fix your issue by adding the parameter -pbCNS to pacBioToCA.

     
  • Sergey Koren
    Sergey Koren
    2014-12-02

    • status: open --> closed
     
  • Sergey Koren
    Sergey Koren
    2014-12-02

    Closing due to inactivity. You can also remove runPartition.sh and re-run the pipeline which will attempt to re-run any missing partitions.