Question: What Is The Directory Structure Required To Run Tophat Fusion?
1
gravatar for AsoInfo
7.5 years ago by
AsoInfo300
Bonn, Germany
AsoInfo300 wrote:

Hi there,

I have ran TopHat successfully with the fusions.out also. But I am unable to understand the directory structure i.e. how to create the directory structure although I have gone through the tutorial but always arising with errors in Tophat fusion.

The created directories are:

./blast_human/human_genomic*, nt* and other_genomic*
tophat_sample11 (containing the output files from TopHat2)
hg19
ensGene.txt
refGene.txt
mcl.txt
./blast/blastall and blastn

whenever I ran the command:

./tophat-fusion-post -o ./FUSIONOUT --num-fusion-reads 1 --num-fusion-pairs 2 --num-fusion-both 5 hg19

the error is:

[Mon Jan 21 16:00:55 2013] Beginning TopHat-Fusion post-processing run (v2.0.6)

[Mon Jan 21 16:00:55 2013] Extracting 23-mer around fusions and mapping them using Bowtie
        samples updated

Traceback (most recent call last):
  File "./tophat-fusion-post", line 2091, in ?
    sys.exit(main())

File "./tophat-fusion-post", line 2059, in main
    map_fusion_kmer(bwt_idx_prefix, params, sample_updated)

File "./tophat-fusion-post", line 315, in map_fusion_kmer
    subprocess.call(cmd, stdout=open(output_dir + 'fusion_seq.bwtout', 'w'), stderr=open('/dev/null', 'w'))

  File "/usr/lib64/python2.4/subprocess.py", line 412, in call
    return Popen(*args, **kwargs).wait()

File "/usr/lib64/python2.4/subprocess.py", line 542, in __init__
    errread, errwrite)

File "/usr/lib64/python2.4/subprocess.py", line 975, in _execute_child
    raise child_exception

OSError: [Errno 2] No such file or directory

No log file is generated.

Thanking in advance!

tophat fusion • 3.4k views
ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by AsoInfo300

Solved....... :)

ADD REPLYlink written 7.5 years ago by AsoInfo300

could you post as an answer what the solution was? May help someone later. Thanks.

ADD REPLYlink written 7.5 years ago by Istvan Albert ♦♦ 84k
2
gravatar for AsoInfo
7.5 years ago by
AsoInfo300
Bonn, Germany
AsoInfo300 wrote:

The error was arising because Bowtie wasn't found in the path. So the path need to be defined as

PATH=$PATH:/path/to/bowtie

It worked for me...

ADD COMMENTlink written 7.5 years ago by AsoInfo300
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