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

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

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?