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Old 04-19-2012, 05:26 PM   #1
Junior Member
Location: USA CA

Join Date: Apr 2012
Posts: 7
Question tophat2 installion problem

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 "$HOME/tophat2/tophat2/bin/tophat", line 3778, in ?
File "$HOME/tophat2/tophat2/bin/tophat", line 3558, in main
args = params.parse_options(argv)
File "$HOME/tophat2/tophat2/bin/tophat", line 901, in parse_options
File "$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

Do you know how can I solve this problem? Many many thanks for your help.
IceWater is offline   Reply With Quote
Old 05-09-2012, 12:09 AM   #2
Junior Member
Location: South Africa

Join Date: Apr 2012
Posts: 5

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 ?
LiamT is offline   Reply With Quote

problem, test data, tophat2

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