[maker-devel] Blastx of repeats with mpi maker failing on small contigs

[Michael Nuhn]

On 04/02/2013 02:01 PM, Eleanor Stanley wrote:
> what version of Blast are you using?
> I was getting similar errors with NCBI BLAST+ 2.2.23 that were resolved using BLAST+ 2.2.27 instead

I was using blast version 2.2.14. I've now swapped it out for ncbi+ 2.2.9.

I am running it on one mpi instance with 128 processors and it seems to 
be working now.

Thanks!
Michael.

> Ele
>
>
> On 2 Apr 2013, at 14:09, Michael Nuhn wrote:
>
>> Hello Carson!
>>
>> (Mpi) Maker (2.27) is failing when it runs blast searches.
>>
>> It prints out the command it is trying to run. When I try to run this command manually on the command line, blast terminates with an error, because it either can't find the input file or it can't find a file ending in .pin, which I think is a protein index file it expects to be there.
>>
>> I've looked at a few contigs on which maker fails and they were all rather short contigs.
>>
>> Maker works fine, if I
>>
>> - run it without mpi or
>> - run it with mpi, but a maximum of 4 processors.
>>
>> (Mpi) Maker used to run fine with 128 processors before this.
>>
>> The contigs are sorted descending by size in the genome file. I think maker has processed the large ones and the problems it is having now might have something to do with it running on smaller contigs.
>>
>>  From looking at the error messages I thought at first the index file of the genome might be corrupted, so I deleted it and let maker rebuild it. This didn't fix the issue though. I have also set the path for temporary files manually to make sure maker is not running out of temporary space.
>>
>> Any idea how to overcome this?.
>>
>> Cheers,
>> Michael.
>>
>> P.S.: A typical error message I'm getting is this:
>>
>> --Next Contig--
>>
>> [blastall] FATAL ERROR:  search cannot proceed due to errors in all contexts/frames of query sequences
>> running  blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /nfs/panda/ensemblgenomes/external/blast/bin/blastall -p blastx -d /nfs/nobackup2/ensemblgenomes/mnuhn/maker/temp2/maker_u5Dl1K/te_proteins%2Efasta.mpi.10.0
>> -i /nfs/nobackup2/ensemblgenomes/mnuhn/maker/temp2/maker_u5Dl1K/rank16/LSalAtl2s8087.0 -b 10000 -v 10000 -e 1e-06 -z 300 -Y 500000000 -a 1 -U -F T -I T -o /n
>> fs/production/panda/ensemblgenomes/development/mnuhn/Sea_louse/test/maker_final_assembly_III/LSalAtl2s.maker.output/LSalAtl2s_datastore/A2/0B/LSalAtl2s8087//
>> theVoid.LSalAtl2s8087/LSalAtl2s8087.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
>> #-------------------------------#
>> ERROR: Chunk failed at level:2, tier_type:0
>> FAILED CONTIG:LSalAtl2s8083
>>
>> doing blastx repeats
>> setting up GFF3 output and fasta chunks
>> doing blastx repeats
>> re reading repeat masker report.
>> /nfs/production/panda/ensemblgenomes/development/mnuhn/Sea_louse/test/maker_final_assembly_III/LSalAtl2s.maker.output/LSalAtl2s_datastore/2C/53/LSalAtl2s8249//theVoid.LSalAtl2s8249/LSalAtl2s8249.0.all.rb.out
>> [blastall] FATAL ERROR:  search cannot proceed due to errors in all contexts/frames of query sequences
>> [blastall] FATAL ERROR:  search cannot proceed due to errors in all contexts/frames of query sequences
>> running  blast search.
>> running  blast search.
>> #--------- command -------------#
>> Widget::blastx:
>> /nfs/panda/ensemblgenomes/external/blast/bin/blastall -p blastx -d /nfs/nobackup2/ensemblgenomes/mnuhn/maker/temp2/maker_u5Dl1K/te_proteins%2Efasta.mpi.10.0 -i /nfs/nobackup2/ensemblgenomes/mnuhn/maker/temp2/maker_u5Dl1K/rank26/LSalAtl2s8135.0 -b 10000 -v 10000 -e 1e-06 -z 300 -Y 500000000 -a 1 -U -F T -I T -o /nfs/production/panda/ensemblgenomes/development/mnuhn/Sea_louse/test/maker_final_assembly_III/LSalAtl2s.maker.output/LSalAtl2s_datastore/EF/10/LSalAtl2s8135//theVoid.LSalAtl2s8135/LSalAtl2s8135.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
>> #-------------------------------#
>> #--------- command -------------#
>> Widget::blastx:
>> /nfs/panda/ensemblgenomes/external/blast/bin/blastall -p blastx -d /nfs/nobackup2/ensemblgenomes/mnuhn/maker/temp2/maker_u5Dl1K/te_proteins%2Efasta.mpi.10.0 -i /nfs/nobackup2/ensemblgenomes/mnuhn/maker/temp2/maker_u5Dl1K/rank19/LSalAtl2s8119.0 -b 10000 -v 10000 -e 1e-06 -z 300 -Y 500000000 -a 1 -U -F T -I T -o /nfs/production/panda/ensemblgenomes/development/mnuhn/Sea_louse/test/maker_final_assembly_III/LSalAtl2s.maker.output/LSalAtl2s_datastore/CA/2E/LSalAtl2s8119//theVoid.LSalAtl2s8119/LSalAtl2s8119.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
>> #-------------------------------#
>> [blastall] FATAL ERROR:  search cannot proceed due to errors in all contexts/frames of query sequences
>> #---------------------------------------------------------------------
>> Now retrying the contig!!
>> SeqID: LSalAtl2s8449
>> Length: 2187
>> Tries: 18!!
>> #---------------------------------------------------------------------
>>
>>
>>
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