Tophat - Bowtie 1: Index Error? What'S Wrong?

Question

[newDNASeqer]

all off sudden, my tophat/bowtie run gives me this error:

Traceback (most recent call last):
  File "/usr/local/bin/tophat-2.0.6/tophat", line 4022, in <module>
    sys.exit(main())
  File "/usr/local/bin/tophat-2.0.6/tophat", line 3822, in main
    check_bowtie(params)
  File "/usr/local/bin/tophat-2.0.6/tophat", line 1490, in check_bowtie
    bowtie_version = get_bowtie_version()
  File "/usr/local/bin/tophat-2.0.6/tophat", line 1366, in get_bowtie_version
    bowtie_out = stdout_value.splitlines()[0]
IndexError: list index out of range

I use tophat 2.0.6 and bowtie 0.12.9 on the server. The index is mouse_ucsc_mm9.

what could be wrong? so frustrating, it has been a few days like this ....

[Devon Ryan]

It's running bowtie --version there, so what's the output of running that? BTW, it'd be helpful if you maintained the error message format.

[newDNASeqer]

bowtie --version returns this result: Illegal instruction

Error message:

Traceback (most recent call last):
  File "/usr/local/bin/tophat-2.0.6/tophat", line 4022, in <module>
    sys.exit(main())
  File "/usr/local/bin/tophat-2.0.6/tophat", line 3822, in main
    check_bowtie(params)
  File "/usr/local/bin/tophat-2.0.6/tophat", line 1490, in check_bowtie
    bowtie_version = get_bowtie_version()
  File "/usr/local/bin/tophat-2.0.6/tophat", line 1366, in get_bowtie_version
    bowtie_out = stdout_value.splitlines()[0]
IndexError: list index out of range

[Devon Ryan]

Then your bowtie install is the problem. Try reinstalling it.

[newDNASeqer]

Yes, after installing a fresh copy of Bowtie, everything is working again. Thanks for help

Answer 1

[Istvan Albert]

What it most likely means that the tool cannot run bowtie and therefore cannot therefore extract the version number from its output.