Hi,
I was just using the new version of Tophat with Samtools-0.1.12a and got the following error:
[Wed Dec 8 16:56:42 2010] Beginning TopHat run (v1.1.4)
-----------------------------------------------
[Wed Dec 8 16:56:42 2010] Preparing output location ./tophat_out/
[Wed Dec 8 16:56:42 2010] Checking for Bowtie index files
[Wed Dec 8 16:56:42 2010] Checking for reference FASTA file
[Wed Dec 8 16:56:42 2010] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Dec 8 16:56:42 2010] Checking for Samtools
Traceback (most recent call last):
File "/share/apps/alignment/tophat/default/bin/tophat", line 2223, in ?
sys.exit(main())
File "/share/apps/alignment/tophat/default/bin/tophat", line 2136, in main
check_samtools()
File "/share/apps/alignment/tophat/default/bin/tophat", line 877, in check_samtools
samtools_version = get_samtools_version()
File "/share/apps/alignment/tophat/default/bin/tophat", line 864, in get_samtools_version
samtools_version = [int(x.split('-')[0]) for x in version_val.split('.')]
ValueError: invalid literal for int(): 12a
Tophat v1.1.4 does work with the previous version of Samtools (Samtools-0.1.11).
Hopefully this bug will be solved.
Alexandra
I was just using the new version of Tophat with Samtools-0.1.12a and got the following error:
[Wed Dec 8 16:56:42 2010] Beginning TopHat run (v1.1.4)
-----------------------------------------------
[Wed Dec 8 16:56:42 2010] Preparing output location ./tophat_out/
[Wed Dec 8 16:56:42 2010] Checking for Bowtie index files
[Wed Dec 8 16:56:42 2010] Checking for reference FASTA file
[Wed Dec 8 16:56:42 2010] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Dec 8 16:56:42 2010] Checking for Samtools
Traceback (most recent call last):
File "/share/apps/alignment/tophat/default/bin/tophat", line 2223, in ?
sys.exit(main())
File "/share/apps/alignment/tophat/default/bin/tophat", line 2136, in main
check_samtools()
File "/share/apps/alignment/tophat/default/bin/tophat", line 877, in check_samtools
samtools_version = get_samtools_version()
File "/share/apps/alignment/tophat/default/bin/tophat", line 864, in get_samtools_version
samtools_version = [int(x.split('-')[0]) for x in version_val.split('.')]
ValueError: invalid literal for int(): 12a
Tophat v1.1.4 does work with the previous version of Samtools (Samtools-0.1.11).
Hopefully this bug will be solved.
Alexandra
Comment