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Trouble running tophat ERROR 105 Unable to locate a modulefile for tophat/2.0.14

Hi there. I am trying to run tophat on RNA-seq reads. I have already ran tophat many times, as I do this pipeline a lot and I never had this problem before.

This is the error 

 : command not foundcurrent/spool/node001/job_scripts/6784818: line 8:
'oduleCmd_Load.c(200):ERROR:105: Unable to locate a modulefile for 'tophat/2.0.14
'oduleCmd_Load.c(200):ERROR:105: Unable to locate a modulefile for 'samtools/0.1.19
: command not foundcurrent/spool/node001/job_scripts/6784818: line 11:
: command not foundcurrent/spool/node001/job_scripts/6784818: line 13:
: command not foundcurrent/spool/node001/job_scripts/6784818: line 14:
/cm/local/apps/sge/current/spool/node001/job_scripts/6784818: line 15: tophat: command not found
: command not foundcurrent/spool/node001/job_scripts/6784818: line 16:
: command not foundcurrent/spool/node001/job_scripts/6784818: line 17:

Before running the script I have already loaded tophat and samstools as I alwayd do. I also tried running the script on a different directory but nothing changes. Can someone please help?

rna-seq tophat
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written by maithex • maithex

Sounds like the module for tophat that you were using may have been deleted. Can you see what you get with module whatis tophat/2.0.14? Same with samtools. These versions are old and deprecated so you should consider upgrading to a newer tool like STAR.

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written by GenoMax GenoMax

Thank you for your reply! I used this module 2 days ago, so I think it is unlikely that it has been deleted, but we never know.

This is what I get:

tophat/2.0.14        : adds TopHat 2.0.14
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written by maithex • maithex

So the module is alive and well. I would say open a new terminal. Load the modules (confirm that they loaded without error) and see if that fixes the issue.

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written by GenoMax GenoMax

I have already done it a couple of times and no success. Tried changing the directories and no success either. Tried googling this error but didnt find much info about.

Yes maybe I will have a look into STAR then Thank you for your attention :)

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written by maithex • maithex

Report this problem to your local sys admins and steps you have already tried. There may be a corruption somewhere in the file system. Sounds like they need to take a look.

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written by GenoMax GenoMax

perhaps try to do a module purge first (this will clear you complete modules environment) and then load the tophat module again.

is it correct the error says "oduleCmd_Load.c .. " (=missing the M in front) or is that a copy-paste error

and as said here as well: you might consider switching to a more modern aligner: STAR, BBmap, HiSat2, ...

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written by lieven.sterck lieven.sterck

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