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widdowquinn / pyani

Application and Python module for average nucleotide identity analyses of microbes.
http://widdowquinn.github.io/pyani/
MIT License
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NUCmer run failure #312

Closed snehamurthy21 closed 3 years ago

snehamurthy21 commented 3 years ago

WARNING: Total alignment length reported in ANI_out/nucmer_output/Aedes-albopictus-C6-36-cell-line_SCAFFOLDS_GCA_001876365.2_vs_GCF_006496715.1_Aalbo_primary.1_genomic.filter is zero! ERROR: This has possibly been a NUCmer run failure, please investigate ERROR: NoneType: None

This is my error for my pyANI

please help me crack this open

I am running ANI for 5 mosquito genomes, 3 are of same species different isolates, 1 is different species and 1 is different mosquito genus.

widdowquinn commented 3 years ago

Hi @snehamurthy21

Thank you for your interest in pyani - this is an interesting issue.

Firstly, I should say that pyani is designed for microbial genomics, and mosquitoes are not microbes. There are major differences between eukaryotic and prokaryotic genomes, and I would not recommend using pyani for eukaryotes (with a few exceptions).

The issue you're seeing right now suggests that there is no identifiable homology between the two sequence files being compared. If you expect that there is in fact some sequence homology there, you could use another comparison tool (e.g. pairwise BLAST) possibly with a suitable visualisation package (e.g. IGV) to get more information. But, for now, it appears that the nucmer comparison pyani is using does not find any significant sequence identity between those sequences.

If you have other genomes in your analysis - and they give good output - you may want to consider dropping one of these sequences.

If your goal is to find a phylogeny for these organisms, I would recommend finding a multigene tree - pyani is not really set up for this kind of comparison between eukaryotes.

Cheers,

L.

snehamurthy21 commented 3 years ago

Thank you for your reply, my bad i didnt realise its specific to microbes, i should have read through

Will definitely do more on the grounds you mention, Thank you once again