[maker-devel] Repeat runner issue

[Pedro Barbosa]

Ok. seems to be related with BLAST then ? I turned the rapsearch flag on
(in the 3.0 beta version) expecting to rapsearch being run over blast.

BLAST options error: File
tmp-dir/maker_k2Axy1/0/blastprep/te_proteins%2Efasta.mpi.10.0 does not exist
ERROR: /opt/tools/ncbi-blast-2.2.31+/bin/makeblastdb failed in
Widget::formater
--> rank=NA, hostname=cebal.example.com
ERROR: Failed while doing blastx repeats
ERROR: Chunk failed at level:1, tier_type:1
FAILED CONTIG:scaffold_1

ERROR: Chunk failed at level:2, tier_type:0
FAILED CONTIG:scaffold_1


Pedro

2015-11-02 16:16 GMT+00:00 Carson Holt <carsonhh at gmail.com>:

> You need to look at your STDERR as the datastorem log just gives you a
> summary of what failed but not why.  The cause of the error will be
> somewhere in your job's STDERR.  You can capture the STDERR to a file by
> redirecting it.
>
> For example, in bash shell —> maker 2> stderr.log
>
> —Carson
>
>
>
> On Nov 2, 2015, at 7:57 AM, Pedro Barbosa <psbpedrobarbosa at gmail.com>
> wrote:
>
> Hello,
>
> I'm unable to run MAKER properly as the datastore_index.log file shows a
> FAILED run for all the scaffolds.
>
> Inspecting the log files from the output directory i see that it always
> dies when repeatrunner is invoked.
>
> *STARTED
> scaff-1k.maker.output/scaff-1k_datastore/3A/5C/scaffold_13//theVoid.scaffold_13/0/scaffold_13.0.consensi%2Efa%2Eclassified%2Empi%2E10%2E9.specific.out*
> *FINISHED
>  scaff-1k.maker.output/scaff-1k_datastore/3A/5C/scaffold_13//theVoid.scaffold_13/0/scaffold_13.0.consensi%2Efa%2Eclassified%2Empi%2E10%2E9.specific.out*
> *STARTED
> scaff-1k.maker.output/scaff-1k_datastore/3A/5C/scaffold_13//theVoid.scaffold_13/0/scaffold_13.0.te_proteins%2Efasta.repeatrunner*
> *DIED    RANK    0:2:0:0*
> *DIED    COUNT   1*
>
> Afterwards, I realized that repeatrunner is no longer included internally
> in MAKER, so I installed and included it in the system path. The error
> remained.
> I tried to remove the parameter 'repeat_protein' from the opts control
> file, because apparently repeatrunner is called when we provide a set of
> transposable elements. No success again.
>
> I tested both with the MAKER v2.31.8 and v3.00.0 beta, but the problem
> doesn't seem to be version related. Please find attached the maker_opts
> file that i used to run.
>
> Could you help me with this ?
>
> Best regards,
> Pedro Barbosa
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>
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