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ParBLiSS / FastANI

Fast Whole-Genome Similarity (ANI) Estimation
Apache License 2.0
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Error: skch::validateInputFiles, Count of query and ref genomes should be non-zero #45

Open kushalgohil opened 5 years ago

kushalgohil commented 5 years ago

I am doing "Many to Many" ANI calculation using fastANI and getting following error,

$ fastANI --ql /home/ncim/ncbi_genomes --rl /home/ncim/ncbi_genomes -o home/ncim/ncbi_genomes/all.out

Reference = [] Query = [] Kmer size = 16 Fragment length = 3000 Threads = 1 ANI output file = home/ncim/ncbi_genomes/all.out

ERROR, skch::validateInputFiles, Count of query and ref genomes should be non-zero

What could go wrong? Please help. When I did "One to One" ANI calculation everything worked fine, but when I am doing many to many ANI calculation I am getting the error.

cjain7 commented 5 years ago

Please carefully follow the instructions in README. The --ql or --rl option expect a text file, with list of genomes. It looks like you are specifying the path to folder where they are saved, which won't work. You would need to create one file, that contains paths to all your genomes.

On linux, following would help ls -1 /home/ncim/ncbi_genomes/* > list_of_genomes.txt