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mbhall88 / drprg

Drug Resistance Prediction with Reference Graphs
https://mbh.sh/drprg/
MIT License
19 stars 1 forks source link

error: unrecognized subcommand 'index' #36

Open ptrmtb opened 10 months ago

ptrmtb commented 10 months ago

Hello, we've been trying to use dr-prg to our research but somehow after installing the program with docker and singularity separately, the index subcommand is not there.. Do you have any idea what went wrong?

iqbal-lab commented 10 months ago

Thanks for trying DrPRG! @mbhall88 is unfortunately on holiday for a couple of weeks, and I think really only he can help. Sorry for the delay!

ptrmtb commented 10 months ago

Hello Iqbal,

Thank you for your quick reply. It's not a problem at all, we researchers need breaks once in a while after all 😃 As alternative we're also currently trying Clockwork for Mycobacterium tuberculosis, and I'm astounded to find out that the link in the official WHO document leads to your GitHub too. I'll let you know if we have succeded on using your program. Thanks for your hard work.

Cheers!

iqbal-lab commented 10 months ago

Hi there! ok good. I just wanted to clarify one thing - DrPRG and clockwork do different things. Clockwork does decontamination of human reads, and SNP/indel calling, and optionally you can run Mykrobe also to predict resistance. But if you just want resistance prediction while waiting for Michael to return, you don't need the whole of clockwork, Mykrobe alone will do. You probably know this, but I just wanted to check (Yes, i was amazed to find the WHO mentioning clockwork!)

mbhall88 commented 10 months ago

Hi @ptrmtb which container are you using? i.e. how are you pulling the container and what address? And what commands are you running to use index and what is the output?