Question: Tophat - Bowtie 1: Index Error? What'S Wrong?
0
gravatar for newDNASeqer
6.3 years ago by
newDNASeqer670
United States
newDNASeqer670 wrote:

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 ....

bowtie • 3.5k views
ADD COMMENTlink modified 6.3 years ago by Istvan Albert ♦♦ 82k • written 6.3 years ago by newDNASeqer670

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.

ADD REPLYlink written 6.3 years ago by Devon Ryan93k

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
ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by newDNASeqer670

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

ADD REPLYlink written 6.3 years ago by Devon Ryan93k

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

ADD REPLYlink written 6.3 years ago by newDNASeqer670
1
gravatar for Istvan Albert
6.3 years ago by
Istvan Albert ♦♦ 82k
University Park, USA
Istvan Albert ♦♦ 82k wrote:

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

ADD COMMENTlink written 6.3 years ago by Istvan Albert ♦♦ 82k
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