linux error while functional annotation

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9.3 years ago

sharma_tina189059 ▴ 50

Can anyone explain this error in linux while using AutoFACT for COG assignment..

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not open <fasta_file: No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:486
STACK: Bio::Root::IO::_initialize_io /usr/local/share/perl5/Bio/Root/IO.pm:351
STACK: Bio::SeqIO::_initialize /usr/local/share/perl5/Bio/SeqIO.pm:491
STACK: Bio::SeqIO::fasta::_initialize /usr/local/share/perl5/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /usr/local/share/perl5/Bio/SeqIO.pm:372
STACK: Bio::SeqIO::new /usr/local/share/perl5/Bio/SeqIO.pm:413
STACK: Utils::get_seqs_in_fasta_file /home/tina/Bioinfo_software/AutoFACT/modules/Utils.pm:341
STACK: /home/tina/Bioinfo_software/AutoFACT/scripts/AutoFACT.pl:60
-----------------------------------------------------------
[tina@tom db_files]$

genome • 2.0k views

ADD COMMENT • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by sharma_tina189059 ▴ 50

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Looks like the input file you are specifying is not present, but I could be wrong.

ADD REPLY • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by Sean Davis 27k

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Maybe the file permission issue or check the path of file as Sean said.

ADD REPLY • link updated 2.1 years ago by Ram 44k • written 9.3 years ago by Zhilong Jia ★ 2.2k

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