Question: question about tophat-fusion error
0
gravatar for syxbestmayer
5.4 years ago by
syxbestmayer10
syxbestmayer10 wrote:

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.

rna-seq • 1.7k views
ADD COMMENTlink modified 3.7 years ago by wade.schulz0 • written 5.4 years ago by syxbestmayer10
0
gravatar for geek_y
5.4 years ago by
geek_y11k
Barcelona
geek_y11k wrote:

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.

ADD COMMENTlink written 5.4 years ago by geek_y11k
0
gravatar for syxbestmayer
5.4 years ago by
syxbestmayer10
syxbestmayer10 wrote:

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

I think my installation has no problem.

ADD COMMENTlink written 5.4 years ago by syxbestmayer10
0
gravatar for wade.schulz
3.7 years ago by
wade.schulz0 wrote:

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.

ADD COMMENTlink written 3.7 years ago by wade.schulz0
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