I am trying to run rMATS to find differentialy expressed splicing isoforms. I get an error in the program that is the same exaclty error when I run the test of instalation and can't figure out the solution. Anybody specialist in rMATS here can helpme?
here is the log file:
2016-03-17 19:28:36,891 start mapping..
2016-03-17 19:28:36,891 bam files are provided. skip mapping..
2016-03-17 19:28:36,891 done mapping..
2016-03-17 19:28:36,891 getting uniquely mapped reads or pairs
2016-03-17 19:28:36,891 getting unique SAM function..
2016-03-17 19:28:38,487 getting uniquely mapped reads or pairs for sample_1, rep_1 is done with status 0
2016-03-17 19:28:38,487
2016-03-17 19:28:40,108 getting uniquely mapped reads or pairs for sample_1, rep_2 is done with status 0
2016-03-17 19:28:40,108
2016-03-17 19:28:41,670 getting uniquely mapped reads or pairs for sample_2, rep_1 is done with status 0
2016-03-17 19:28:41,670
2016-03-17 19:28:43,243 getting uniquely mapped reads or pairs for sample_2, rep_2 is done with status 0
2016-03-17 19:28:43,244
2016-03-17 19:28:43,244 done getting unique SAM files..
2016-03-17 19:28:43,248 start getting AS events from GTF and SAM files
2016-03-17 19:28:43,248 getting AS events function..
2016-03-17 19:28:43,309 getting AS events is done with status 256
2016-03-17 19:28:43,310 error in getting AS events 256
2016-03-17 19:28:43,310 error detail: Traceback (most recent call last):
File "/home/tiagocastro/atalhos/programs/rMATS.3.2.1.beta/bin/processGTF.SAMs.py", line 119, in <module>
group = range(int(sC)/chunk, int(eC)/chunk + 1); ## groups this line could belong to
TypeError: 'float' object cannot be interpreted as an integer
2016-03-17 19:28:43,310 There is an exception in getting AS events
2016-03-17 19:28:43,310 Exception: <type 'exceptions.Exception'>
2016-03-17 19:28:43,310 Detail:
Are you using python3? If so, try this with python2 instead.