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veg / hivtrace

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Error during tn93 steps #65

Closed lexleong closed 4 years ago

lexleong commented 4 years ago

Hi veg,

I have installed the hivtrace onto my computer without any issue. However, when I tried running it against one of my fasta sequences, it came back with an error during the tn93 steps (refer below). $ hivtrace -i ./1932701285MUAL.fasta -a resolve -r HXB2_prrt -t .015 -m 500 -g .05 -c Traceback (most recent call last): File "/home/iidlleo/.local/bin/hivtrace", line 10, in <module> sys.exit(main()) File "/home/iidlleo/.local/lib/python3.7/site-packages/hivtrace/hivtrace.py", line 840, in main attributes_file=ATTRIBUTES_FILE) File "/home/iidlleo/.local/lib/python3.7/site-packages/hivtrace/hivtrace.py", line 561, in hivtrace raise Exception(' '.join(tn93_process) + "returned empty file") Exception: tn93 -q -o /tmp/hivtrace-dks3vvkf/1932701285MUAL.fasta_user.tn93output.csv -t .015 -a resolve -l 500 -g .05 -f csv ./1932701285MUAL.fasta_output.fastareturned empty file

It looks like it has to do with some empty file that is not looking right. I wonder if anyone can help me out?

Cheers, Lex

stevenweaver commented 4 years ago

Dear @lexleong,

Have you installed tn93 on your machine? Unfortunately, tn93 must be installed separately. Instructions can be found in the README.

Please let me know if that was the issue.

Best, Steven

lexleong commented 4 years ago

Hi @stevenweaver,

I have downloaded tn93 to my server before running the hivtrace.

But, I figured out this problem has plenty to do with my naivety/stupidness in HIV analysis. In my fasta file, there were only 1 unaligned sequence. After testing the program with several aligned sequences, HIV-trace ran without any error!

Sorry, I jumped too quicky... Cheers, Lex