Hi guys,

is anybody use tophat-fusion?

I use 'tophat-2.0.11.Linux_x86_64' ran my RNA-seq data get some error like:

Traceback (most recent call last):
  File "/usr/local/bin/tophat-fusion-post", line 2647, in <module>
    sys.exit(main())
  File "/usr/local/bin/tophat-fusion-post", line 2615, in main
    map_fusion_kmer(bwt_idx_prefix, params, sample_updated)
  File "/usr/local/bin/tophat-fusion-post", line 325, in map_fusion_kmer
    subprocess.call(cmd, stdout=open(output_dir + 'fusion_seq.bwtout', 'w'), stderr=open('/dev/null', 'w'))
  File "/usr/lib64/python2.6/subprocess.py", line 478, in call
    p = Popen(*popenargs, **kwargs)
  File "/usr/lib64/python2.6/subprocess.py", line 642, in __init__
    errread, errwrite)
  File "/usr/lib64/python2.6/subprocess.py", line 1234, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

The command I used is :

tophat-fusion-post -p 8 --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 medaka

is anybody know how to fix it?

Thanks a million.