[maker-devel] Repeat runner issue

[Pedro Barbosa]

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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