tophat2 installion problem

[IceWater]

Hi All,

When installing TopHat2, a problem occurred in the test step. When I run tophat2 with the test data from Tophat website, I got the following error:

Traceback (most recent call last):
File "$HOME/tophat2/tophat2/bin/tophat", line 3778, in ?
sys.exit(main())
File "$HOME/tophat2/tophat2/bin/tophat", line 3558, in main
args = params.parse_options(argv)
File "$HOME/tophat2/tophat2/bin/tophat", line 901, in parse_options
self.read_params.parse_options(opts)
File "$HOME/tophat2/tophat2/bin/tophat", line 381, in parse_options
self.mate_inner_dist = int(value)
ValueError: invalid literal for int(): test_ref

Other dependencies:
bowtie 0.12.7
boost_1_49_0
samtools-0.1.18

Do you know how can I solve this problem? Many many thanks for your help.

[LiamT]

Hi IceWater

Perhaps you could post the command line code you used to run the test data. Also, are your test_data indexes .bt2 or .ebwt in extension ?