<p>I am trying to predict transmembrane protein using <code>tmhmm-2.0c</code>. According to Package instruction, I have changed the path of perl inside the program like as following:</p>
<p>First i checked the location of perl</p>
<pre><code>which perl
/usr/bin/perl
</code></pre>
<p>Then I checked the version also to make sure it is above 5.</p>
<pre><code>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
</code></pre>
<p>I have pasted the path (<code>/usr/bin/perl</code>) in the <code>tmhmm</code> and <code>tmhmmformat.pl</code>
Run the cmd:</p>
<pre><code>./tmhmm --short &lt; /mnt/genome3/Lab_Users/Kishor/DISK_3/mnspt1/blood/rsem_outdir/blood.Trinity.RSEM.retained.clustered.fasta.transdecoder.pep &gt; tmhmm.out
</code></pre>
<p>But I only received a blank folder. It will be great for me if I get any suggestions to solve the problem.</p>

CC BY-SA 4.0
2021-10-08T14:34:01.140Z
You're right about the Perl path, both in the tmhmm and the tmhmmformat.pl file, but if you select the short option you will not get the output to create the output plot in the folder, that is why is empty.
zorbax
CC BY-SA 4.0
2021-10-08T16:46:30.473Z
Thanks Zora. But also tried without setting parameter '--short' and still didnt find output except a blank folder. I actually need following typr of output to fed into Trinotate:





TRINITY_DN100_c0_g1_i1.p1 len=115 ExpAA=0.00 First60=0.00 PredHel=0 Topology=i

TRINITY_DN102_c0_g2_i1.p1 len=256 ExpAA=0.16 First60=0.07 PredHel=0 Topology=o

TRINITY_DN103_c0_g1_i1.p1 len=107 ExpAA=16.73 First60=0.00 PredHel=0 Topology=o


Can you give me any other suggestion?
Kishor Kumar Sarker
CC BY-SA 4.0
2021-10-08T17:07:41.973Z
can you share minimal input to reproduce your error?
zorbax
CC BY-SA 4.0
2021-11-24T17:35:59.337Z
@zorbax
Thanks for your concern. I have solved the issue. Needed to do some change inside the  tmhmm program.
Kishor Kumar Sarker
CC BY-SA 4.0
2021-12-15T05:37:19.467Z
Hi Kishor Kumar Sarker What changes you had done inside the tmhmm program?????? I also got the empty folder.
Dimple
Dimple
CC BY-SA 4.0
2021-12-16T11:17:35.577Z
Hi @Dimple,
In following link you will find the detail about the problem and as well as the solution at the end.
https://github.com/Trinotate/Trinotate/issues/77
Kishor Kumar Sarker
<linux><software-installation><perl>
tmhmm installation and running
# tmhmm installation and running

(Asked by: username_0 on 2021-10-08)

I am trying to predict transmembrane protein using tmhmm-2.0c. According to Package instruction, I have changed the path of perl inside the program like as following:
First i checked 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.

**Tags:** linux, software-installation, perl
> **Comments:**
> **username_1**: You're right about the Perl path, both in the tmhmm and the tmhmmformat.pl file, but if you select the short option you will not get the output to create the output plot in the folder, that is why is empty.  
> **username_0**: Thanks Zora. But also tried without setting parameter '--short' and still didnt find output except a blank folder. I actually need following typr of output to fed into Trinotate:      TRINITY_DN100_c0_g1_i1.p1 len=115 ExpAA=0.00 First60=0.00 PredHel=0 Topology=i  TRINITY_DN102_c0_g2_i1.p1 len=256 ExpAA=0.16 First60=0.07 PredHel=0 Topology=o  TRINITY_DN103_c0_g1_i1.p1 len=107 ExpAA=16.73 First60=0.00 PredHel=0 Topology=o   Can you give me any other suggestion?  
> **username_1**: can you share minimal input to reproduce your error?  
> **username_0**: @zorbax Thanks for your concern. I have solved the issue. Needed to do some change inside the  tmhmm program.  
> **username_2**: Hi Kishor Kumar Sarker What changes you had done inside the tmhmm program?????? I also got the empty folder. Dimple  
> **username_0**: Hi @Dimple, In following link you will find the detail about the problem and as well as the solution at the end. https://github.com/Trinotate/Trinotate/issues/77  

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## 0 answers

