getting no output for genome files about fastani HOT 9 CLOSED

Also noticing a similar issue. Thanks in advance for any help!

from fastani.

Hi, FastANI reports ANI for genomes related within ~80 - 100% nucleotide identity range. Otherwise no output is given.

Can you try using alternative implementation and please confirm me if this is the case? Or alternatively share the input genomes here.

For diverge genome sequences outside 80-100 ANI range, computing identity at amino acid level is recommended in the literature.

I will revise documentation to avoid this misunderstanding :)

from fastani.

@jotech I notice the data you gave me. I confirmed at my end that the two genomes lack 80-100% ANI.

I tried Blast-based ANI and got following output

$ ruby enveomics/Scripts/ani.rb -1 BT247.fasta -2 MYb12.fasta
Insuffient hits to estimate one-way ANI: 9.
Insuffient hits to estimate one-way ANI: 15.
Insufficient hits to estimate two-way ANI: 6

Will make this clear in README.

from fastani.

Thank you so much, this makes sense! I'm now having a look on amino acid identity (aai from enveomics). Do you know whether the values from ani and aai are comparable? So could I use ani and for lower identity aai to get a consistent phylogenetic distance?

from fastani.

Do you know whether the values from ani and aai are comparable?
Yes, I believe they are.

Quoting from this paper Bypassing Cultivation To Identify Bacterial Species:
The analysis shows that ANI offers robust resolution between genomes that share 80–100% ANI, i.e., within species or among closely related species, and that species that share less than 80% ANI and/or 30% of their gene content are too divergent to be compared based on the ANI measurement. For the latter genomes, AAI provides a much more robust resolution and should be used instead.

from fastani.

just came back. Thanks for this clarification!

from fastani.

Hi
I run this command : ./fastANI --ql ../1.fasta --rl ../2.fasta -o output
I obtain
Threads = 1
ANI output file = output

ERROR, skch::validateInputFiles, Could not open >Scaffold_1

I don't no why he could not open the file 1 ?

from fastani.

@diaz13 , it seems like you wish to do one-to-one comparison, for that you should be running ./fastANI -q ../1.fasta -r ../2.fasta -o output

from fastani.

@cjain7, thank you. I had not paid attention.
I have a list of 400 genomes but it's good to run , for now no problem.

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