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Psy-Fer / deeplexicon

Signal based nanopore RNA demultiplexing with convolutional neural networks
https://psy-fer.github.io/deeplexicon/
MIT License
36 stars 8 forks source link

multi-threading is not working #19

Open lucacozzuto opened 2 years ago

lucacozzuto commented 2 years ago

Dear authors, I used multi-threading and I got only a few reads generated. While removing that option gives me no error. Also using -t 1 is generating an error.

Thanks, Luca

Psy-Fer commented 2 years ago

Hello,

Could you please give me the full command you used, and with which version of the software, as well as any errors you are encountering.

Thanks, James

ps @lpryszcz could you please keep an eye on this one :)

lucacozzuto commented 2 years ago

I'm using the image from @lpryszcz actually. The command line is the following

deeplexicon_sub.py dmux -f multi -m resnet20-final.h5 -t 1 -p ./ > pU---1_demux.tsv
Psy-Fer commented 2 years ago

Ahh, deeplexicon_sub.py doesn't have a -t for threads, but for a --test command.

please use deeplexicon_multi.py with --threads argument

lucacozzuto commented 2 years ago

Aha! Can I suggest changing this as well? This is a bit misleading :) Sorry for this but it took me a day to figure it out the problem :)

lpryszcz commented 2 years ago

I'm sorry Luca. I kept old version for back-compatibility (I guess older versions are still needed for training of the model). Everything is described in the README https://github.com/Psy-Fer/deeplexicon#source-and-install-requirements-gpu-experimental @Psy-Fer could you please update the documentation accordingly (https://psy-fer.github.io/deeplexicon/)?

Psy-Fer commented 2 years ago

Yep,. I'm on break at the moment and will be back in the new year. We can probably remove the test flag too so we can free up the -t argument for threads