Trouble running tophat ERROR 105 Unable to locate a modulefile for tophat/2.0.14
0
0
Entering edit mode
16 months ago
maithex • 0

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 • 709 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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
ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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 :)

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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, ...

ADD REPLY

Login before adding your answer.

Traffic: 1886 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6