[maker-devel] Repeat runner issue

[Carson Holt]

RepeatRunner requires BLAST regardless. RapSearch on the beta version will run for the protein alignment (even then I’ve found it prone to failure and it actually runs slower than BLAST on some longer sequences).

If there is an issue with your own BLAST installation you can let MAKER install it’s own BLAST (some versions of BLAST+ do have issues).  Go to the maker source directory and run './Build blast’. It will install BLAST+ in …/maker/exe/blast. It will be version 2.2.28.  This is because a couple of the newer updates to BLAST+ actually have bugs and spurious warnings/errors.

—Carson



> On Nov 2, 2015, at 9:28 AM, Pedro Barbosa <psbpedrobarbosa at gmail.com> wrote:
> 
> 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 <http://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 <mailto: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 <mailto: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
>> <maker_opts.ctl>_______________________________________________
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> 
> 

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