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genome1 04-18-2014 12:19 PM

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>
File "./tophat", line 4050, in main
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/", line 642, in __init__
errread, errwrite)
File "/usr/lib64/python2.6/", 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.

dpryan 04-18-2014 02:07 PM

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.

genome1 04-19-2014 12:15 PM

No there were enough space in the disk. Now the problem has been resolved.
I have replaced tophat with tophat2 in the command line.

konika 10-15-2014 02:53 AM

Tophat error about samtools version
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:
[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>
File "/appl/bio/tophat/tophat-2.0.11.Linux_x86_64/tophat", line 3882, in main
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( for x in [1,2,3]]
AttributeError: 'NoneType' object has no attribute 'group'

Any ideas?

GenoMax 10-15-2014 06:48 AM

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).

konika 10-15-2014 07:14 AM

Thanks, I used the older version of samtools and it fixed.

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