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iqbal-lab-org / pandora

Pan-genome inference and genotyping with long noisy or short accurate reads
MIT License
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warnings while doing VCF calls with pandora map #206

Closed LilithElina closed 4 years ago

LilithElina commented 4 years ago

I finally got around to try the --genotype argument in pandora map and while I got the expected two VCF files as output, I also had a lot of warnings in the console. They were always these two for different (probably all, I didn't count) genes:

[2020-01-08 09:32:57.905378] [0x00007fd741ceff80] [warning] Input vcf_ref path was too short to be the ref for PRG GC00002025

[2020-01-08 09:32:57.905389] [0x00007fd741ceff80] [warning] Could not find reference sequence for GC00002025 in the PRG so using the consensus path

They occur after this line:

Wed Jan 8 09:32:57 2020 Find PRG paths and write to files:

This did not happen when I used pandora map without the --genotype option. What does it mean?

rmcolq commented 4 years ago

These warnings can safely be ignored. They are being triggered by the default user behaviour which is not to provide a VCF reference. The first of these is already fixed in a pull request I'm waiting to merge in. We will update the code to stop the second being triggered also (or at least call it something other than warning)

LilithElina commented 4 years ago

Thank you!