Problem with samtools

[maxineumeh]

Hi all,

I am very new to using the Tuxedo programs and I am running into the following error when trying to run tophat2:

raiden:my_rnaseq_exp maxine$ tophat2 -p 8 -G genes.gtf -o C1_R1_thout genome C1_R1_1.fq C1_R1_2.fq

[2014-07-08 15:03:38] Beginning TopHat run (v2.0.12)
-----------------------------------------------
[2014-07-08 15:03:38] Checking for Bowtie
Bowtie version: 2.2.3.0
[2014-07-08 15:03:38] Checking for Samtools
Traceback (most recent call last):
File "/Network/Servers/raiden.genomecenter.ucdavis.edu/Users/maxine/Program/tophat", line 4087, in <module>
sys.exit(main())
File "/Network/Servers/raiden.genomecenter.ucdavis.edu/Users/maxine/Program/tophat", line 3885, in main
check_samtools()
File "/Network/Servers/raiden.genomecenter.ucdavis.edu/Users/maxine/Program/tophat", line 1559, in check_samtools
samtools_version_str, samtools_version_arr = get_samtools_version()
File "/Network/Servers/raiden.genomecenter.ucdavis.edu/Users/maxine/Program/tophat", line 1541, in get_samtools_version
samtools_version_arr = [(version_match.group(x)) for x in [1,2,3]]
AttributeError: 'NoneType' object has no attribute 'group'

I am not sure why this is occurring. Earlier today I created aliases to python2.7 so that tophat would use that version instead of python3.2 which is on our server. Because that was giving me an getopt.error message. So now that error is resolved but this new error is produced.

Any help would be greatly appreciated!

Thank you
Maxine