QIIME: OTU-picking works way too long
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4.9 years ago
lotus28 ▴ 70

I am trying to use pick_closed_reference_otus QIIME script to assign taxonomy to single-direction 16S RNA-reads.
To do so, I downloaded the latest 13_8 Greengenes DB. I decided to test it with a small datasset in Virtual Box QIIME:

pick_closed_reference_otus.py -i /media/sf_ena/test/small_filtered.txt -o /media/sf_ena/OUT_otus -r /media/sf_ena/otus.fna -t /media/sf_ena/otus.txt -p /media/sf_ena/test/PARAMS


The script seems to take in all the parameters, runs with almost 4GB of RAM, but nothing happens even after much time.
I'm trying to assign taxonomy literally to just 2 reads, but it doesn't work.

Will it be any different if I use QIIME not in Virtual Box? What might be the problem?
Or how can I identify the problem?

qiime otu 16s • 1.6k views
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Locate the logs in output dir and read them

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Logs stop at the point when I press enter.

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