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pcantalupo / annotater

Annotate sequences by BLAST using NCBI taxonomy information
MIT License
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getting multiple "print() on closed filehandle TMPOUT" messages #1

Closed pcantalupo closed 7 years ago

pcantalupo commented 7 years ago

i'm seeing multiple messages like this during Taxonomy step

print() on closed filehandle TMPOUT at /path/to/annotater/Reann.pm line 275, <IN> line 17

which is followed by this exception:

------------- EXCEPTION -------------
MSG: Could not read file '~/path/to/viral.1.1.genomic.fna.gis.txt.fa': No such file or directory
STACK Bio::Root::IO::_initialize_io /path/to/bioperl/bioperl-live/Bio/Root/IO.pm:268
STACK Bio::SeqIO::_initialize /path/to/bioperl/bioperl-live/Bio/SeqIO.pm:513
STACK Bio::SeqIO::fasta::_initialize /path/to/bioperl/bioperl-live/Bio/SeqIO/fasta.pm:87
STACK Bio::SeqIO::new /path/to/bioperl/bioperl-live/Bio/SeqIO.pm:389
STACK Bio::SeqIO::new /path/to/bioperl/bioperl-live/Bio/SeqIO.pm:435
STACK Reann::Taxonomy /path/to/annotater/Reann.pm:282
STACK toplevel /path/to/annotater/Reann.pl:17
-------------------------------------
pcantalupo commented 7 years ago

This happens when using a tilde for user home directory in config file for path to blast database. Example:

~/path/to/viral.1.1.genomic.fna