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mcveanlab / mccortex

De novo genome assembly and multisample variant calling
https://github.com/mcveanlab/mccortex/wiki
MIT License
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mccortex31 check: report error if records incomplete. #84

Closed izaak-coleman closed 5 years ago

izaak-coleman commented 5 years ago

I just wanted a sanity check - because i'm running on an unstable cluster that kills processes randomly - will mccortex31 check test a .ctx to see whether some preceding mccortex31 command successfully wrote all kmer records it intended to write to the .ctx? Or will it just check header corruption. I can see how corruption in the head could be tested (there are two CORTEX tags bounding the head). But is there a similar structure to check all intended kmer records were written?

iqbal-lab commented 5 years ago

it checks all the records are ok; it can't check that it is a correctly built graph from the input data, but it checks that it is all valid

izaak-coleman commented 5 years ago

So, if mccortex31 build was writing a .ctx and killed during the write process (so, only half the records were output), assuming that all written records were ok, would mccortex31 check detect the corruption? Thanks for your reply!

iqbal-lab commented 5 years ago

Yes, that's one thing we use it for

izaak-coleman commented 5 years ago

Great! Thanks Professor Iqbal.