[maker-devel] Repeat runner issue

[Carson Holt]

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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