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

[Carson Holt]

Good to know.

Thanks,
Carson


On 13-04-02 10:38 AM, "Michael Nuhn" <mnuhn at ebi.ac.uk> wrote:

>
>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/LSal
>>>Atl2s8087.0 -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/make
>>>r_final_assembly_III/LSalAtl2s.maker.output/LSalAtl2s_datastore/A2/0B/LS
>>>alAtl2s8087//
>>> 
>>>theVoid.LSalAtl2s8087/LSalAtl2s8087.0.te_proteins%2Efasta.repeatrunner.t
>>>emp_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/ma
>>>ker_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/LSal
>>>Atl2s8135.0 -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/ma
>>>ker_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/LSal
>>>Atl2s8119.0 -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/ma
>>>ker_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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>>
>>
>>
>
>
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