Getting errors trying to run rmats

Question

[Omnia]

Hi,

I am trying to use rmats for splice variation analysis through ssh using slurm

after loading rmats module, these are commands that I tried and errors they produced

rmats --s1 $PWD/control.txt --s2 $PWD/pdac.txt --gtf mm10/mm10.refGene.gtf

Python programming language version 3.6.8 loaded. GNU Scientific Library (GSL) version 2.3 loaded. htseq version 0.13.5 loaded. samtools version 1.9 loaded. star version 2.7.3a loaded. rmats version 4.0.2 loaded. /var/spool/slurm/d/job940099/slurm_script: line 5: rmats: command not found

run_rmats --s1 $PWD/control.txt --s2 $PWD/pdac.txt --gtf mm10/mm10.refGene.gtf

-bash: run_rmats: command not found

I tried to run it as rmats. py, this produced this error

Python programming language version 3.6.8 loaded. GNU Scientific Library (GSL) version 2.3 loaded. htseq version 0.13.5 loaded. samtools version 1.9 loaded. star version 2.7.3a loaded. rmats version 4.0.2 loaded. File "/N/soft/rhel7/rmats/4.0.2/rMATS-turbo-Linux-UCS2/rmats.py", line 31 print "mapping the first sample" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("mapping the first sample")?

Answer 1

[patrickdm]

Hello, the last error message

File "/N/soft/rhel7/rmats/4.0.2/rMATS-turbo-Linux-UCS2/rmats.py", line 31 print "mapping the first sample" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("mapping the first sample")?

is telling you that there is a SyntaxError in rmats.py: it states that parentheses are missing for a print call at line 31. If you have access to the rmats.py script you could add them (as suggested in the message above), or I guess you will have to notify the administrators about the issue to have it fixed.

[i.sudbery]

This suggests to me that the rmats script that is being used was written for python 2, not python 3. As the latest version of rmates is python 3 compatible, that suggests to me that an old version of rmats is being used.