Hi I'm hoping someone can help me trouble shoot this.
I installed bowtie, samtool, boost and tophat as suggested on http://ccb.jhu.edu/software/tophat/tutorial.shtml. Everything went well, but when I run the test, I got the following error message. I guess something is run with the Samtools? but I'm not sure what the issue is. I searched previous posts regarding tophat installation but none seems to help. I'd really appreciate any help.
[2014-09-12 17:29:53] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2014-09-12 17:29:53] Checking for Bowtie
Bowtie version: 2.2.3.0
[2014-09-12 17:29:53] Checking for Samtools
Traceback (most recent call last):
File "/Users/xx/bin/tophat", line 4087, in <module>
sys.exit(main())
File "/Users/xx/bin/tophat", line 3885, in main
check_samtools()
File "/Users/xx/bin/tophat", line 1559, in check_samtools
samtools_version_str, samtools_version_arr = get_samtools_version()
File "/Users/xx/bin/tophat", line 1541, in get_samtools_version
samtools_version_arr = [int(version_match.group(x)) for x in [1,2,3]]
AttributeError: 'NoneType' object has no attribute 'group'
I installed bowtie, samtool, boost and tophat as suggested on http://ccb.jhu.edu/software/tophat/tutorial.shtml. Everything went well, but when I run the test, I got the following error message. I guess something is run with the Samtools? but I'm not sure what the issue is. I searched previous posts regarding tophat installation but none seems to help. I'd really appreciate any help.
[2014-09-12 17:29:53] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2014-09-12 17:29:53] Checking for Bowtie
Bowtie version: 2.2.3.0
[2014-09-12 17:29:53] Checking for Samtools
Traceback (most recent call last):
File "/Users/xx/bin/tophat", line 4087, in <module>
sys.exit(main())
File "/Users/xx/bin/tophat", line 3885, in main
check_samtools()
File "/Users/xx/bin/tophat", line 1559, in check_samtools
samtools_version_str, samtools_version_arr = get_samtools_version()
File "/Users/xx/bin/tophat", line 1541, in get_samtools_version
samtools_version_arr = [int(version_match.group(x)) for x in [1,2,3]]
AttributeError: 'NoneType' object has no attribute 'group'
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