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nanoporetech / dorado

Oxford Nanopore's Basecaller
https://nanoporetech.com/
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Order of flags importance #101

Closed pwh124 closed 6 months ago

pwh124 commented 1 year ago

Hello,

We have noticed that the order of the flags matters when running Dorado, especially the --modified-bases option. We have seen this same behavior with previous versions as well as v0.2.1.

For example, when I run:

~/software/dorado_0.2.1/bin/dorado basecaller --verbose -x "cuda:all" --num_runners 8 --modified-bases 5mCG_5hmCG ~/software/dorado_0.2.1/models/dna_r10.4.1_e8.2_400bps_sup@v4.0.0 {pod5}.pod5 >  {output}.sam

I get the following error

[2023-02-16 09:37:35.844] [error] '/home/phook2/software/dorado_0.2.1/models/dna_r10.4.1_e8.2_400bps_sup@v4.0.0' is not a supported modification please select from 5mCG, 5mCG_5hmCG

And when I flip the --modified-bases flag to another position, like so:

~/software/dorado_0.2.1/bin/dorado basecaller --verbose -x "cuda:all" --modified-bases 5mCG_5hmCG --num_runners 8 ~/software/dorado_0.2.1/models/dna_r10.4.1_e8.2_400bps_sup@v4.0.0 {pod5}.pod5 >  {output}.sam

It begins to run.

Paul

vellamike commented 1 year ago

Hi @pwh124 - this definitely sounds like a bug. We are looking into it.

iiSeymour commented 1 year ago

Thanks @pwh124 there is a little more detail here https://github.com/nanoporetech/dorado/issues/56#issuecomment-1343445514