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YangLab / CLEAR

direct comparison of circular and linear RNA expression
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tophat fusion error #16

Open sharmi85 opened 3 years ago

sharmi85 commented 3 years ago

I have installed all the bowtie, tophat and samtool packages recommended for the tophatfusion run, but getting this error, it cant locate my samtools. I have version you have asked to install...Kindly help

Beginning TopHat run (v2.0.12)

[2021-01-09 16:21:33] Checking for Bowtie Bowtie version: 1.0.0.0 [2021-01-09 16:21:33] Checking for Samtools Traceback (most recent call last): File "/userdata/sharmishtha/tools/tophat-2.0.12.Linux_x86_64/tophat", line 4087, in sys.exit(main()) File "/userdata/sharmishtha/tools/tophat-2.0.12.Linux_x86_64/tophat", line 3885, in main check_samtools() File "/userdata/sharmishtha/tools/tophat-2.0.12.Linux_x86_64/tophat", line 1559, in check_samtools samtools_version_str, samtools_version_arr = get_samtools_version() File "/userdata/sharmishtha/tools/tophat-2.0.12.Linux_x86_64/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'

sharmi85 commented 3 years ago

I have the following versions tophat2：tophat-2.0.12.Linux_x86_64 samtools：0.1.18.0 bowtie：1.0.0.0

bio-visualisation commented 3 years ago

I have the following versions tophat2：tophat-2.0.12.Linux_x86_64 samtools：0.1.18.0 bowtie：1.0.0.0

I used tophat 2.1.0 along with python 2.7 , samtools- 0.1.18 and bowtie- 1.0.0 ; It worked for me. I encountered tophat fusion error with other version of tophat2. Hope this helps.