Comments (3)
This is exactly what the code performs for you. Each line in the clusters.tsv file is one vOTU. The first column is the vOTU representative, and the second column is the vOTU members.
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Thanks for the reply, but when I run cluster.py, 0 edges appear inside, is it normal?
`python cluster.py --fna viruses.fna --ani ani.tsv --out clusters.tsv --min_ani 95 --min_qcov 0 --min_tcov 85
reading sequences...
7983 sequences retained from fna
time: 0.04 seconds, peak RAM: 0.01 GB
storing edges...
0 edges retained from blastani
0 edges currently stored
time: 0.07 seconds, peak RAM: 0.01 GB
clustering...
7983 total clusters
time: 0.07 seconds, peak RAM: 0.01 GB
writing clusters...
time: 0.07 seconds, peak RAM: 0.01 GB`
Here's my output of the cluster.tsv file,and the two columns are the same.
clusters.zip
I'm sorry to bother you.
Best Wishs!
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No that is not expected, likely because your ani.tsv
file is empty. Try using an updated script and directions here: https://bitbucket.org/berkeleylab/checkv/src/master/#markdown-header-supporting-code
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