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

[Carson Holt]

Could you set the TMP= option to a non-NFS mounted location (the default
/tmp should work) and let me know if it still fails?

You can also try completely deleting the
LSalAtl2s.maker.output/mpi_blastdb directory before restarting.

Thanks,
Carson



On 13-04-02 9:09 AM, "Michael Nuhn" <mnuhn at ebi.ac.uk> 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%2
>Efasta.mpi.10.0 
>
>-i 
>/nfs/nobackup2/ensemblgenomes/mnuhn/maker/temp2/maker_u5Dl1K/rank16/LSalAt
>l2s8087.0 
>-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/LSalAt
>l2s8087//
>theVoid.LSalAtl2s8087/LSalAtl2s8087.0.te_proteins%2Efasta.repeatrunner.tem
>p_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/make
>r_final_assembly_III/LSalAtl2s.maker.output/LSalAtl2s_datastore/2C/53/LSal
>Atl2s8249//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%2
>Efasta.mpi.10.0 
>-i 
>/nfs/nobackup2/ensemblgenomes/mnuhn/maker/temp2/maker_u5Dl1K/rank26/LSalAt
>l2s8135.0 
>-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/make
>r_final_assembly_III/LSalAtl2s.maker.output/LSalAtl2s_datastore/EF/10/LSal
>Atl2s8135//theVoid.LSalAtl2s8135/LSalAtl2s8135.0.te_proteins%2Efasta.repea
>trunner.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%2
>Efasta.mpi.10.0 
>-i 
>/nfs/nobackup2/ensemblgenomes/mnuhn/maker/temp2/maker_u5Dl1K/rank19/LSalAt
>l2s8119.0 
>-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/make
>r_final_assembly_III/LSalAtl2s.maker.output/LSalAtl2s_datastore/CA/2E/LSal
>Atl2s8119//theVoid.LSalAtl2s8119/LSalAtl2s8119.0.te_proteins%2Efasta.repea
>trunner.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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