Activity for ViReMa
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ViReMa updated /ViReMa_0.29/ViReMa_0.29.zip
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Doeun posted a comment on discussion General Discussion
I attempted to detect virus integration sites using ViReMa by using the example sample in the source code file. The test run was successful without any errors. However, when I tried using my own samples, the bed file was not generated correctly, so I am reaching out for help. I executed the following command: /home/kde/anaconda3/envs/virema/bin/ViReMa.py \ --Host_Index /home/kde/PROJECTS/VirusIntegrationTools/HBV_C/hg19 \ /home/kde/PROJECTS/VirusIntegrationTools/download/ViReMa/reference/AB033550_padded...
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Julia Hillung posted a comment on discussion General Discussion
Hi, a colleague took over the project and as I can remember it was a problem of versions of programs. You need exactly the versions of programs (bowtie etc..) that are specified for Virema. She created a kind of an extra environment to make the computer acces the correct versions of the programs for running Virema. I hope it helps. If you need I can ask her for more details. cheers, Julia
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Nan Jiang posted a comment on discussion General Discussion
Hi, I got the same error! have you figured out how to solve it?
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Hey, I am very green in bioinformatics, please help! I am trying to run virema with the Test Data and get the error at the end: ('Aligner Directory =', '/Users/evolsysvir10/Desktop/bowtie-0.12.9/') ('Output Directory =', '') Virus Index Found Beginning alignments on Chunk Number 1 10000 reads in input file. 6733 reads remaining to be aligned after first iteration. Traceback (most recent call last): File "ViReMa.py", line 1182, in <module> IterateAlignments('ChunkedReads') File "ViReMa.py", line 1124,...
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