[maker-devel] Repeatmasker error?

[Freeman, Robert M.]

Greetings,

Am using MAKER 2.27b to annotate a ciliate genome and am finding that my log files are growing to GB sizes. When looking more carefully, an error seems to be occurring around the Repeatmasker stage:

....
Now starting the contig!!
--

setting up GFF3 output and fasta chunks
doing repeat masking
doing blastx repeats
doing blastx of proteins
doing blastx of proteins
doing blastx of proteins
doing blastx repeats
collecting blastx repeatmasking
processing all repeats
ERROR: Can't open seq file: /files/.retain-snapshots.d14d-w60d/SysBio/klab_genome/maker/stentor/run_current_r3/soapPrice1.cycle7.maker.output/soapPrice1.cycle7_datastore/03/EF/contig_157//theVoid.contig_157/query.masked.gff.seq
No such file or directory

 at /groups/acornworm/opt/maker-2.27-beta/bin/../lib/Dumper/GFF/GFFV3.pm line 182
        Dumper::GFF::GFFV3::finalize('Dumper::GFF::GFFV3=HASH(0x50547f8)') called at /groups/acornworm/opt/maker-2.27-beta/bin/../lib/Process/MpiChunk.pm line 691
        Process::MpiChunk::__ANON__() called at /groups/acornworm/opt/maker-2.27-beta/bin/../lib/Error.pm line 415
        eval {...} called at /groups/acornworm/opt/maker-2.27-beta/bin/../lib/Error.pm line 407
        Error::subs::try('CODE(0x5b859c0)', 'HASH(0x11ea63f0)') called at /groups/acornworm/opt/maker-2.27-beta/bin/../lib
...

I don't seem to have this problem when I fall back to the 2.25b version (though I start having major DBD:SQLite issues).

I'm doing this on a cluster, running this under MPI with 50 cores.

Any help/suggestions would be appreciated!

-Bob

-----------------------------------------------------
Bob Freeman, Ph.D.
Acorn Worm Informatics, Kirschner lab
Dept of Systems Biology, Alpert 524
Harvard Medical School
200 Longwood Avenue
Boston, MA  02115
617/432.2294, vox

"Sorry I'm late. Oh, God, that sounded insincere. I'm late."
-- Karen Walker, from Will and Grace



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