Question: When running maker, how is the *.index files in fold mpi_blastdb/ generated?
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gravatar for gerrychang1985
2.9 years ago by
gerrychang198530 wrote:

Hi,everyone,

Do anyone know how are the *.index files in <input fasta="">.maker.output/mpi_blastdb/ generated when running maker annotation?

Actually, my maker software went wrong after a recent update of our system,the error message is listed below:

<h6>#</h6>

STATUS: Parsing control files... INFO: All repeat masking options will be skipped.

STATUS: Processing and indexing input FASTA files...

------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Could not open index file /lfs1/backup/F13ZHQYJSY1409/changyue/Nitrogen/Datisca_glomerata/DNA/01.annotation/platanus_1st/01.gene/01.maker/all_soft_final/new_machine/running/Dg_1st_allsoft.fa.46/Dg_1st_allsoft.fa.maker.output/mpi_blastdb/Dg_1st_allsoft%2Efa%2E46.mpi.1/Dg_1st_allsoft%2Efa%2E46.mpi.1.0.index: Function not implemented STACK: Error::throw STACK: Bio::Root::Root::throw /ifs1/ST_PLANT/USER/changyue/Program/bigones/Perl/lib/perl5/site_perl/5.22.0/Bio/Root/Root.pm:449 STACK: Bio::DB::IndexedBase::_open_index /ifs1/ST_PLANT/USER/changyue/Program/bigones/Perl/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:666 STACK: Bio::DB::IndexedBase::_index_files /ifs1/ST_PLANT/USER/changyue/Program/bigones/Perl/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:656 STACK: Bio::DB::IndexedBase::index_file /ifs1/ST_PLANT/USER/changyue/Program/bigones/Perl/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:484 STACK: Bio::DB::IndexedBase::new /ifs1/ST_PLANT/USER/changyue/Program/bigones/Perl/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:364 STACK: FastaDB::_safe_new /ifs1/ST_PLANT/USER/changyue/Program/maker/bin/../lib/FastaDB.pm:204 STACK: FastaDB::new /ifs1/ST_PLANT/USER/changyue/Program/maker/bin/../lib/FastaDB.pm:45 STACK: GI::build_fasta_index /ifs1/ST_PLANT/USER/changyue/Program/maker/bin/../lib/GI.pm:1894 STACK: /ifs1/ST_PLANT/USER/changyue/Program/maker/bin/maker:539

<h6>#</h6>

I think the cause is the *.index file in mpi_blastdb/. The file was generated, but the size is different from the right one. I suppose the *.index was not properly written, but could not check it because it is binary.

Thank you

maker gene annotation • 903 views
ADD COMMENTlink written 2.9 years ago by gerrychang198530
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