no tmhmm output

[shruti choudhary]

Dear Trinity users

I am running the tmhmm command in the directory where the software is located:

tmhmm --short < transdecoder.pep > tmhmm.out

 

But my tmhhm.out is empty

 

Can anyone help me out with this?

[Brian Haas]

Hi Schruti,

Do you get an error message when trying to run it?

~b

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Brian J. Haas
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[Shruti Choudhary]

There was no error message. The output file is there after few secs of running the command, but it's empty.

One thing I had not done was not to include the directory of tmhmm in my path. Since, I was running the command in the tmhmm itself, I felt that wasn't necessary. So I guess it had nothing to do with it.

     Another thing,iIn the tmhmmformat.pl, there are:

gnuplot = "/usr/local/bin/gnuplot-3.7 ";
$epsmove = "/sbin/grep -v \'translate\$\' ";
$ps2gif = "/usr/local/bin/gs -dNOPAUSE -q -sDEVICE=ppm -g710x350 -r72 -sOutputFile=- - -c quit | /usr/freeware/bin/ppmtogif - ";

Do their path need corrections too?

--Shruti

[Brian Haas]

Hi Shruti,

I don't remember there being any serious tweaking to their code to get it to work.  In our documentation, we just have:

tmhmm v2 (free academic download) http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm

You might need to edit the header lines of the scripts 'tmhmm' and 'tmhmmformat.pl' to read:
#!/usr/bin/env perl

You might try contacting their help support to work through any kinks.


best,


~brian

[Rudolf Majer]

I had the exact same problem once.

It turned out I did the same thing you did: I forgot to load the path to tmhmm-2.0c/bin into the $PATH variable.
From your answer I could not conclude whether you eventually added it to $PATH and tried again?
If not you should try that.

The paths in tmhmmformat.pl should be correct unless you installed another version of gnuplot or not to the standard directory.

[Brian Haas]

Your invocation of tmhmm should be:

    tmhmm --short < transdecoder.pep > tmhmm.out

The 'tmhmm' script that comes with the tmhmm software distribution appears to find the other tools where they exist in the bundle.


best,

~b

On Fri, Jul 15, 2016 at 5:20 PM, Mounika Atmala <lakshmi....@gmail.com> wrote:
>
> can someone help me out with TMHMM installation. I had changed the header file path and path to main directory of software.
> when I run the command: cat seq.fasta  | decodeanhmm -f <path>/TMHMM2.0.options -modelfile <path>/TMHMM2.0.model
> decodeanhmm: command not found error

[ck chaudhary]

Hi shruti

I got the same problem. Just add the full path to tmhmm binary. It will run like anything.

good luck

On Wednesday, April 20, 2016 at 8:10:40 PM UTC+5:30, shruti choudhary wrote:

[Karen Rossmassler]

Hi all,

Has anyone been able to solve this? I followed their installation instructions to edit the tmhmm and tmhmmformat.pl, and added the full path to the tmhmm binary. I still get an entirely empty tmhmm.out file. So, there is no error message, but the program is still not running.

Thanks,

Karen

[Brian Haas]

One trick with this is to install tmhmm directly from its package and put the entire package somewhere (don't just move parts of it).   

Edit any scripts as directed.

Then, run tmhmm by giving the full path to it.  

ie.  /usr/local/tmhmmpackage/bin/tmhmm

hope this helps,

~brian

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[Loubna Youssar]

copying the whole package to /usr/local worked for me. The other options were not successful.

Many thanks

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