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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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Having problem with average_nucleotide_identity.py #131

Closed sushanta26 closed 5 years ago

sushanta26 commented 5 years ago

Hi I was trying to get ANI value for 33 bacterial species ,but when I run the "average_nucleotide_identity.py" command system shows following error message.Please correct me If I am making any mistake in command. pyani was installed using pip3

Command is average_nucleotide_identity.py -i /home/sdas/Desktop/test_ani_data/ --blastn_exe /home/sdas/Desktop/ANI/ncbi-blast-2.6.0+/bin/ -l /home/sdas/Desktop/logfile -o /home/sdas/Desktop/output/all -m ANIb

Error: WARNING: At least one BLAST run failed. ANIb may fail.

Python Version: 3

Operating System:linux (readhat)

widdowquinn commented 5 years ago

Hi @sushanta26 - thank you for your using pyani.

This error tends to come up when using pyani to calculate ANI for bacterial isolates with essentially zero sequence identity. This can show up as an absence of BLAST output, which pyani then interprets as a failed BLAST job (BLAST jobs can fail for numerous reasons).

I would suggest inspecting the logfile to see which BLAST jobs were run, and comparing the expected output filenames to those that were written (and seeing if any have zero content). Then try running the BLAST commands corresponding to the empty files/missing output.

If the BLAST run completes successfully, but there is no output, then it might be best to exclude at least one of the genomes you were using from the analysis.

widdowquinn commented 5 years ago

I'm assuming for now that the issue was with the input dataset. Please reopen if the advice above did not solve your issue.