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Old 04-18-2014, 12:19 PM   #1
genome1
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Location: India

Join Date: Oct 2013
Posts: 12
Default Tophat2: OSError: [Errno 2] No such file or directory

I am having a trouble while running tophat2.
I am using tophat2 (v2.0.11), Bowtie2 (v2.2.2) and samtools (v0.1.19).
The command line that I am using is as follows:
$ tophat -G /path/to/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf --transcriptome-index /path/to/transcriptome_data/known -o /path/to/out -p 8 /path/to/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/genome /path/to/read_1.fastq.gz /path/to/read_2.fastq.gz

The last few lines of the error message is:

[2014-04-18 01:59:45] Resuming TopHat pipeline with unmapped reads
Traceback (most recent call last):
File "./tophat", line 4084, in <module>
sys.exit(main())
File "./tophat", line 4050, in main
user_supplied_deletions)
File "./tophat", line 3452, in spliced_alignment
if not nonzeroFile(initial_reads[0]) and \
File "./tophat", line 1159, in nonzeroFile
samtools_view = subprocess.Popen(samtools_view_cmd, stdout=subprocess.PIPE)
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

Can anyone of you help me to solve the problem.
Thank you.
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Old 04-18-2014, 02:07 PM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,476
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Was the disk you were using full? It's trying to open a file that it should have just created but can't. The most likely explanation is that the disk is full.
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Old 04-19-2014, 12:15 PM   #3
genome1
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Location: India

Join Date: Oct 2013
Posts: 12
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No there were enough space in the disk. Now the problem has been resolved.
I have replaced tophat with tophat2 in the command line.
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Old 10-15-2014, 02:53 AM   #4
konika
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Location: Norway

Join Date: Sep 2010
Posts: 14
Default Tophat error about samtools version

Hi
I have tried using tophat2 but still got a similar error
tophat2 -r 20 test_ref reads_1.fq reads_2.fq

[2014-10-15 12:50:45] Beginning TopHat run (v2.0.11)
-----------------------------------------------
[2014-10-15 12:50:45] Checking for Bowtie
Bowtie version: 2.1.0.0
[2014-10-15 12:50:45] Checking for Samtools
Traceback (most recent call last):
File "/appl/bio/tophat/tophat-2.0.11.Linux_x86_64/tophat", line 4084, in <module>
sys.exit(main())
File "/appl/bio/tophat/tophat-2.0.11.Linux_x86_64/tophat", line 3882, in main
check_samtools()
File "/appl/bio/tophat/tophat-2.0.11.Linux_x86_64/tophat", line 1556, in check_samtools
samtools_version_str, samtools_version_arr = get_samtools_version()
File "/appl/bio/tophat/tophat-2.0.11.Linux_x86_64/tophat", line 1538, in get_samtools_version
samtools_version_arr = [int(version_match.group(x)) for x in [1,2,3]]
AttributeError: 'NoneType' object has no attribute 'group'


Any ideas?
Thanks
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Old 10-15-2014, 06:48 AM   #5
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,550
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Are you using new samtools (v.1.x) by chance? TopHat is likely incompatible with the latest samtools (they are now bundling an older version of samtools in TopHat downloads).

You are running an old Tophat version BTW (current is v.2.0.13).
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Old 10-15-2014, 07:14 AM   #6
konika
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Location: Norway

Join Date: Sep 2010
Posts: 14
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Thanks, I used the older version of samtools and it fixed.
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bioinformactics, rna-seq, rna-seq data analysis, tophat2

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