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CPTR-ReSeqTB / UVP

Mycobacterium tuberculosis next generation sequence analysis
MIT License
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gatk3/gatk3-register and gatk/gatk-register #29

Open alantsangmb opened 4 years ago

alantsangmb commented 4 years ago

Hi, I am installing UVP-2.7.0 following the conda installation instruction. However, only gatk3 and gatk3-register are found in the /bin directory in the uvp-2.7.0 conda env. So error occur when gatk-register and gatk are executed.

Is there any difference between gatk3 and gatk? How can I install gatk-register/gatk instead of gatk3-register/gatk3? Thank you.

alantsangmb commented 4 years ago

Sorry that I found I am still wrongly calling the uvp v2.6.0 instead of v2.7.0. So the gatk3 issue should be irrelevant. Thank you.

alantsangmb commented 4 years ago

I have re-installed the UVP 2.7.0 again. I have used gatk3-register to register the GenomeAnlysisTK.jar file. And I have changed to use gatk3 instead of gatk by modifying the snp.py script.

UVP ran normally until the final stage of running genome coverage statistics, following error occur: ################### File " /ReSeqTB/UVP/uvp/snp.py", lilne 511, in runCoverage if cov != '' and int(cov) < 10: ValueError: invalid literal for int() with base 10: '72.06139252064278\n' ###################

The coverage of this sample is an integer of 72 reported in the _Coverage.txt file when I ran this sample using UVP 2.5.1 previously.

Did I do anything wrong?