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Old 01-21-2013, 02:58 AM   #1
AsoBioInfo
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Location: KSA

Join Date: Dec 2011
Posts: 37
Default Tophat-fusion-post error

Hi all,

I know my question is a very naive and basic and I know, something is just wrong with the directories creation.

I am working with Tophat v2.0.6. I already ran tophat2 with bowtie1 and got the fusions.out file.

While using ./tophat-fusion-post, the error is arising at the first step.

The folder tree is as below:

TopHat Linux (Main directory)
  • hg19 bowtie1 index
    ensGene.txt
    refGene.txt
    fusions.out
    blastall
    blastn
    ./blast_human/human_genomic*, nt*, other_genomic*

The error message is:
[Mon Jan 21 13:09:33 2013] Beginning TopHat-Fusion post-processing run (v2.0.6)
-----------------------------------------------
[Mon Jan 21 13:09:33 2013] Extracting 23-mer around fusions and mapping them using Bowtie
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

On the TopHat page, it is mentioned as:
Install BLAST binaries (blastall and blastn).
Make (top_dir)/blast directory, download human_genomic*, other_genomic*, and nt* from blast database, and extract them under (top_dir)/blast_human.

blastall and blastn should be in the blast folder? To be very honest, I am unable to understand the folders creation.

Thanking in advance.
Aso

Last edited by AsoBioInfo; 01-21-2013 at 03:03 AM. Reason: Completing it
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Old 01-29-2013, 03:40 AM   #2
AsoBioInfo
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Location: KSA

Join Date: Dec 2011
Posts: 37
Default

It's solved......
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Old 02-21-2013, 04:59 PM   #3
dingying85
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Location: Pittsburgh

Join Date: Jan 2012
Posts: 3
Default

Quote:
Originally Posted by AsoBioInfo View Post
It's solved......
May I ask how to solve the problem. I got the same problem
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Old 07-13-2014, 03:40 AM   #4
jp.
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Location: NikoNarita.jp

Join Date: Jul 2013
Posts: 142
Default

Quote:
Originally Posted by AsoBioInfo View Post
It's solved......
Can you please post solution.. I have same error
thank you
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Old 12-23-2014, 02:19 AM   #5
IdoSloma
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Location: israel

Join Date: Jun 2013
Posts: 2
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File "/apps/tophat2//tophat-fusion-post", line 937, in alignments_region
popen = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=open('/dev/null'))


Problem is related to subprocess module in python. Go to line 937 and add shell=True at the end.

subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=open('/dev/null'),shell=True)


This solved mine.
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