test Tophat ERROR

Question

[sjing2003]

Dear all,

I have installed tophat2 and tested it with the test_data. It couldn't work and reported error logs as follow:

[2014-04-23 11:08:39] Beginning TopHat run (v2.0.11)
-----------------------------------------------
[2014-04-23 11:08:39] Checking for Bowtie
          Bowtie version:     2.1.0.0
[2014-04-23 11:08:39] Checking for Samtools
        Samtools version:     0.1.19.0
[2014-04-23 11:08:39] Checking for Bowtie index files (genome)..
    Found both Bowtie1 and Bowtie2 indexes.
[2014-04-23 11:08:39] Checking for reference FASTA file
[2014-04-23 11:08:39] Generating SAM header for ./test_data/test_ref
[2014-04-23 11:08:39] Preparing reads
     left reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
    right reads: min. length=75, max. length=75, 100 kept reads (0 discarded)
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 3499, in spliced_alignment
    if reads == None or not nonzeroFile(reads):
  File "./tophat", line 1159, in nonzeroFile
    samtools_view = subprocess.Popen(samtools_view_cmd, stdout=subprocess.PIPE)
  File "/usr/lib/python2.7/subprocess.py", line 679, in __init__
    errread, errwrite)
  File "/usr/lib/python2.7/subprocess.py", line 1259, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

I have to idea to solve this problems. Could you please give me some advice?

best regards,
Jing Shang

[Asaf]

Can you paste the command line you ran?

Answer 1

[Floris Brenk]

Usually a problem between saying tophat vs tophat2

http://seqanswers.com/forums/showthread.php?t=42592

http://seqanswers.com/forums/showthread.php?t=33258