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")?
1 answer
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.
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