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ParBLiSS / FastANI

Fast Whole-Genome Similarity (ANI) Estimation
Apache License 2.0
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Program runs, but output file is empty. #34

Closed vinisalazar closed 5 years ago

vinisalazar commented 5 years ago

Hi,

I'm running FastANI, the console logs indicate it appears to be working fine, but the output fine is empty. Command: FastANI -q GCF_000063525.1_ASM6352v1_genomic.fna -r GCF_002356215.1_ASM235621v1_genomic.fna -o ani_test.txt

Console: `

Reference = [GCF_002356215.1_ASM235621v1_genomic.fna] Query = [GCF_000063525.1_ASM6352v1_genomic.fna] Kmer size = 16 Fragment length = 3000 Threads = 1 ANI output file = ani_test.txt

INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 249756 INFO [thread 0], skch::Sketch::index, unique minimizers = 245256 INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (1, 241440) ... (12, 2) INFO [thread 0], skch::Sketch::computeFreqHist, With threshold 0.001%, ignore minimizers occurring >= 12 times during lookup. INFO [thread 0], skch::main, Time spent sketching the reference : 0.361363 sec

INFO [thread 0], skch::main, Time spent mapping fragments in query #1 : 0.211354 sec INFO [thread 0], skch::main, Time spent post mapping : 2.0606e-05 sec `

After this, ani_test.txt is empty.

I also had some problems trying to run with -ql and -rl params, but I will prep an issue later.

Thanks,

V

vinisalazar commented 5 years ago

Sorry, I just noticed #21 and #22 are similar to this.

vinisalazar commented 5 years ago

I'd just like to add that changing --fragLen to 200 made it work.

cjain7 commented 5 years ago

We are currently looking into extending FastANI to protein level for handling divergent genomes (<80% similarity).

vinisalazar commented 5 years ago

That is great to hear, I'd suggest opening the issues here, I'm sure there are people willing to colaborate