FastANI Blank output/finished without producing output

Question

[Neel]

Hi, I am trying to run FastANI and it run perfectly but it produced blank/Empty output even i tried at AAI amino acid level still result are same, what i can do ?

fastANI -q /home/neel@m95/Desktop/AMR/annotated/fna/1.txt --rl  /home/neel@m95/Desktop/AMR/refgenome/2.txt -o output_2.txt
>>>>>>>>>>>>>>>>>>
Reference = [GCA_000006765.1_ASM676v1_genomic.fna]
Query = [/home/neel@m95/Desktop/AMR/annotated/fna/1.txt]
Kmer size = 16
Fragment length = 3000
Threads = 1
ANI output file = output_2.txt
>>>>>>>>>>>>>>>>>>
INFO [thread 0], skch::main, Count of threads executing parallel_for : 1
INFO [thread 0], skch::Sketch::build, window size for minimizer sampling  = 24
INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 501302
INFO [thread 0], skch::Sketch::index, unique minimizers = 477392
INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (1, 458218) ... (18, 1)
INFO [thread 0], skch::Sketch::computeFreqHist, consider all minimizers during lookup.
INFO [thread 0], skch::main, Time spent sketching the reference : 1.04382 sec
INFO [thread 0], skch::main, Time spent mapping fragments in query #1 : 0.000250891 sec
INFO [thread 0], skch::main, Time spent post mapping : 1.33e-06 sec
INFO [thread 0], skch::main, ready to exit the loop
INFO, skch::main, parallel_for execution finished

Thank you

Answer 1

[Mensur Dlakic]

I think the program will output something only when the similarity is greater than 70-75%. It can be tested that the program works by using the same query and reference file.

Separately, if this is a metagenome comparison you may want to lower the --fragLen value from a default 3000 to 1000-2000.

[Neel]

Actually i wanna do pan genome comparison. Thank you for your time, it will be very helpful for me.