[maker-devel] bioperl problem?

[Carson Holt]

All of the errors seem to be more IO related.  No indication of errors
from BioPerl.

Could you make sure your /tmp directory is not full and that that it is
locally mounted (for example some systems have /tmp mounted as in memory
virtual drives).  Use Œdf -h /tmp¹ to check both.

Finally what version of MAKER are you running?  Could you check to make
sure it is the latest 2.30.

Thanks,
Carson



On 12/22/13, 2:35 PM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:

>Hello all,
>
>We have MAKER installed on our supercomputing cluster, and I used it
>successfully this past summer.  I tried it again yesterday, and although
>MAKER appears to have finished annotating all the scaffolds (see attached
>datastore index) it seems to get stuck afterwards due to some kind of
>bioperl error and never actually finishes.  None of the
>"all.maker.transcripts.fasta","all.maker.snap_masked.proteins.fasta"
>files, etc. have been produced. Is the best answer to reinstall BioPerl?
>Any other thoughts I can pass on to our IT guys?
>
>Best wishes, Jackie
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