Entering edit mode
3.0 years ago
kishorssf91
▴
20
Hi,
I am trying to predict transmembrane protein using tmhmm-2.0c. I have changed the path of perl like as following.
#First i check the location of perl
which perl
/usr/bin/perl
#Then i checked the version also to make sure it is above 5.
perl -v
This is perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi
(with 44 registered patches, see perl -V for more detail)
Copyright 1987-2012, Larry Wall
#I have pasted the path (/usr/bin/perl) in the tmhmm and tmhmmformat.pl
# Run the cmd:
./tmhmm --short < /mnt/genome3/Lab_Users/Kishor/DISK_3/mnspt1/blood/rsem_outdir/blood.Trinity.RSEM.retained.clustered.fasta.transdecoder.pep > tmhmm.out
But i only received a blank folder. It will be great for me if i get any suggestions to solve the problem. Thanks
Some general debugging steps:
Is the tool supposed to output an entire directory of files? What is the expected output?
Did you check the contents of
tmhmm.out
? Was anything printed to the console since your STDERR is not captured in a file?