question about tophat-fusion error

Question

[syxbestmayer]

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.

Answer 1

[GouthamAtla]

OSError: [Errno 2] No such file or directory.

Are you sure the files are in the right path?

Can you just run tophat-fusion-post to see if the installation is successful? You should see the help message and other options.

[syxbestmayer]

can you tell me what is the meaning of the files in the right path?

I think my installation has no problem.

Answer 2

[wade.schulz]

While this question is a bit old, the error may be referring to the subprocess cmd not being found (in this case, likely Bowtie). tophat-fusion-post needs bowtie v1 (rather than bowtie2), so make sure it's present on your path if anyone else runs into the same issue.