tmhmm installation and running

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4.1 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

tmhmm • 2.1k views

ADD COMMENT • link updated 4.1 years ago by Ram 45k • written 4.1 years ago by kishorssf91 ▴ 20

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Entering edit mode

Some general debugging steps:

I only received a blank folder

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?

ADD REPLY • link 4.1 years ago by Ram 45k

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