getting multiple "print() on closed filehandle TMPOUT" messages
pcantalupo opened this issue · 1 comments
pcantalupo commented
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
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