[maker-devel] ./FINISHED/FINISHED.gff

[Carson Holt]

Sometime the master_datastore_index.log gets munged by MPI (processes print
at the same time).  You can rebuild it by running a single instance of maker
whith the -dsindex flag.  It only takes about 60 seconds to rebuild.

Example:
cd <directory where you run maker>
maker -dsindex

--Carson


From:  Yunfei Guo <guoyunfei1989 at gmail.com>
Date:  Friday, 24 May, 2013 12:15 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] ./FINISHED/FINISHED.gff

Hi Carson,

When I tried to merge all gff files, I got this error:

ERROR: The file './FINISHED/FINISHED.gff' does not exist

and I found something like below in master_datastore_index.log. Is this
caused by the duplicate scaffold?

C12919781       GapCloser-Nigro-Min1k_datastore/28/79/C12919781/
FINISHED
        FINISHED
scaffold138015  GapCloser-Nigro-Min1k_datastore/F7/0C/scaffold138015/
FINISHED


FASTA lines for C12919781  and scaffold138015

>C12919781 36.0
>C12919781 36.0
CGTAAATGCATCCGCGTATAAATGCGACAGTAAGAGTTAATGATGCAGTATAAAAAGCAAGAAAAAGCGTTTATGG
TGGGAGGCGGAGGCATCCAACTAACACCAGACTGTTAACCCGGAGACCAGTGGTCGACACCGTCG(skip...)
>scaffold138015 35.1
ATATGCATATGCATATGCATATGCATATGCATATGCATATATAGACATGTAGATATAGACATCAATCATACACGTA
ACCCATCATTCGTATTATTAAATCACATTTTGTGACTTTGCCCATCTGTCTTTAAAGGGACAATGTGTATG(skip
...)

maker 2.27

Thanks,
Yunfei
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