Re: [wgs-assembler-users] chunks failed in cns stage : perl interpreter - permission denied

[Rui-Peng W. <rui...@gm...>]

Thanks for the suggestion but it did not help..

I restarted runPartition.sh by specifying the failed chunk (i.e #26) .
Although it did not complain about the perl interpreter the final
output.fasta and output.qual returned empty. I do see another stderr from :

26.lay.err

Parsing arguments
Opening stores
Loading library information
Streaming fragments
openLayFile()-- Failed to open '/data/../tempLib/asm.26.olaps' for reading:
No such file or directory
Couldn't open '/data/../tempLib/asm.26.olaps' for read No such file or
directory

Is there way to reproduce these asm*.olaps files again. So I can restart
runPartition.sh on the failed chunks with succes. At the momentI have only
2 failed chunks out of 140 but still 60 chunks are being processed.



On Thu, Dec 18, 2014 at 12:02 AM, Serge Koren <ser...@gm...> wrote:
>
> This is most likely due to a missing or different perl on some of your
> cluster nodes. You can try logging into the nodes on which the chunks are
> failing to see if you can run/access the specified perl path. If a
> consistent set of nodes is failing, you could also restrict the
> runPartition.sh script to only run on a subset of your machines where it
> works. If it only happens for a small subset of chunks, you can re-run the
> failed ones manually using the runPartition.sh script. Just specify the
> missing chunk on the command line:
> cd temp<library name>
> sh runPartiton.sh <failed chunk #>
>
> Sergey
>
> > On Dec 17, 2014, at 6:25 AM, Rui-Peng Wang <rui...@gm...>
> wrote:
> >
> > Hello,
> >
> > I am running PBcR using MHAP. It is currently in the PBcR CNS stage.
> Currently 53 chunks out of 200 are being processed. Three chunks are
> finished, however two of them returned this message in stderr:
> >
> > /opt/sge/default/pool/Node028/job_scripts/246889:
> /data/rp/tools/wgs-8.2/Linux-amd64/bin/convertToPBCNS:
> /opt/smrtanalysis/miscdeps/basesys/usr/bin/perl: bad interpreter:
> Permission denied
> >
> > The strange thing is one chunk took 4 hours and it finished successfully
> with a generated trim.fasta file. The failed chunks did not generate
> trim.fasta but there is a broken symlink..
> >
> > We have tested our SGE system with a dummy perl script (a modified copy
> of convertToPBCNS)  and all our nodes did not complain about the perl
> interpreter.
> >
> > Can someone help me how to deal with this and can I continue with the
> CNS stage process?
> >
> >
> >
> >
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