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[BUG] anvi-dereplicate-genomes does not accept float in --min-fraction #2342

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u-xixi opened this issue Sep 17, 2024 · 0 comments
Open

[BUG] anvi-dereplicate-genomes does not accept float in --min-fraction #2342

u-xixi opened this issue Sep 17, 2024 · 0 comments

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@u-xixi
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u-xixi commented Sep 17, 2024

Short description of the problem

anvi-dereplicate-genomes raises an error when giving a float to --min-fraction

anvi'o version

Anvi'o .......................................: marie (v8-dev)
Python .......................................: 3.10.12

Profile database .............................: 40
Contigs database .............................: 24
Pan database .................................: 21
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 4
tRNA-seq database ............................: 2

System info

Run within anvio conda environment on an HPC system using rhel

Detailed description of the issue

anvi-dereplicate-genomes -i selected_bins.txt -o anvi-out --program fastANI --min-fraction 0.1 -T 30 --similarity-threshold 0.9 --cluster-method simple_greedy --representative-method Qscore raised an error :
anvi-dereplicate-genomes: error: argument --min-fraction: invalid int value: '0.1'.

Then I changed it to --min-fraction 10. There was no error but no clustering happened. I switched to dRep using similar parameters and the clusters were formed.

So there seems to be a small bug in the flag --min-fraction.

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