Entering edit mode
3.9 years 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?
Sounds like the module for
tophatthat you were using may have been deleted. Can you see what you get withmodule whatis tophat/2.0.14? Same withsamtools. These versions are old and deprecated so you should consider upgrading to a newer tool likeSTAR.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:
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.
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 :)
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.
perhaps try to do a
module purgefirst (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 errorand as said here as well: you might consider switching to a more modern aligner: STAR, BBmap, HiSat2, ...