Blank output

[jayrbolton]

In certain (fairly rare) cases, I'm finding blank output from certain fasta data.

Example query file: https://github.com/jayrbolton/random-test-data/blob/master/fasta/shewanella.fasta Example reference file: https://github.com/jayrbolton/random-test-data/blob/master/fasta/rhodobacter.fasta

Commands to reproduce

$ fastANI -q shewanella.fasta -r rhodobacter.fasta -o result.out
$ cat result.out

The file is empty. The stdout is:

>>>>>>>>>>>>>>>>>>
Reference = [rhodobacter.fasta]
Query = [shewanella.fasta]
Kmer size = 16
Fragment length = 3000
Threads = 1
ANI output file = result.out
>>>>>>>>>>>>>>>>>>
INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 368426
INFO [thread 0], skch::Sketch::index, unique minimizers = 352326
INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (1, 339338) ... (26, 1)
INFO [thread 0], skch::Sketch::computeFreqHist, With threshold 0.001%, ignore minimizers occurring >= 20 times during lookup.
INFO [thread 0], skch::main, Time spent sketching the reference : 0.306699 sec
INFO [thread 0], skch::main, Time spent mapping fragments in query #1 : 0.269743 sec
INFO [thread 0], skch::main, Time spent post mapping : 2.426e-05 sec

At first I thought this had to do with lowercase/uppercase nucleotides in the fasta, but that does not seem to make a difference.

[cjain7]

No ANI output is reported for a genome pair if ANI value is much below 80%. Such case should be computed at amino acid level. (Also mentioned in the README file). Could you check the AAI between the two genomes? If it turns out to be more than 80%, then it's an issue in FastANI.

[jayrbolton]

Thanks, I must've missed that sentence in the docs. Closing I can check AAI but I am sure it is below 80

[cjain7]

Okay. I think that's a useful feedback. It would be useful to incorporate AAI computation within FastANI itself at some point.

[peterjc]

See also #19 on missing output for poor aligments