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Core BioPerl 1.x code
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Bio::DB::IndexedBase unable to open index file #303

Closed walkeryp closed 5 years ago

walkeryp commented 5 years ago 
use Bio::DB::Fasta;
test <- Bio::DB::Fasta->new("dir/to/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa")

and I get the following output

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not open index file /hwfssz1/ST_PRECISION/PMO/F16ZQSB1SY2968/3.scripts/2.Neoantigen/classI/version3/database/cache/homo_sapiens_merged/92_GRCh38/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.index: Inappropriate ioctl for device
STACK: Error::throw
STACK: Bio::Root::Root::throw /hwfssz1/ST_PRECISION/USER/liwenhui/01.Software/03.packages/Perlpackage/perl5/lib/perl5/Bio/Root/Root.pm:447
STACK: Bio::DB::IndexedBase::_open_index /hwfssz1/ST_PRECISION/USER/liwenhui/01.Software/03.packages/Perlpackage/perl5/lib/perl5/Bio/DB/IndexedBase.pm:712
STACK: Bio::DB::IndexedBase::_index_files /hwfssz1/ST_PRECISION/USER/liwenhui/01.Software/03.packages/Perlpackage/perl5/lib/perl5/Bio/DB/IndexedBase.pm:689
STACK: Bio::DB::IndexedBase::index_file /hwfssz1/ST_PRECISION/USER/liwenhui/01.Software/03.packages/Perlpackage/perl5/lib/perl5/Bio/DB/IndexedBase.pm:525
STACK: Bio::DB::IndexedBase::new /hwfssz1/ST_PRECISION/USER/liwenhui/01.Software/03.packages/Perlpackage/perl5/lib/perl5/Bio/DB/IndexedBase.pm:405
cjfields commented 5 years ago

Hi @Lypzero, you have a bit of mixing with R and Perl here, do you mean:

use Bio::DB::Fasta;
my $test = Bio::DB::Fasta->new("dir/to/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa")

?

cjfields commented 5 years ago

Hi @Lypzero the above version works for me using the latest Gencode GRCh38 release. If this is still an issue feel free to reopen this ticket.