search

nanoporetech / bonito

A PyTorch Basecaller for Oxford Nanopore Reads
https://nanoporetech.com/
Other
381 stars 118 forks source link

can't locate attribute: 'sample_id' #334

Closed NiteshCCMB closed 1 year ago

NiteshCCMB commented 1 year ago

Hi, I am trying to do basecalling using Bonito on the nanopore-wgs-consortium NA12878 dataset. But I am getting the can't locate attribute: 'sample_id' error. Is there something I can do to make it work or to debug the issue.

sachingadakh commented 1 year ago

Hello Nitesh, did you resolve the issue I am facing the same issue with the same dataset you mentioned

onkar2470 commented 1 year ago

Hi Sachin, Yes, we were able to solve the issue. We have written a Python script which adds sample_id information to older fast5 files. The script is publically available on GitHub: https://github.com/SowpatiLab/ONT_scripts

sachingadakh commented 1 year ago

Thank you so much Onkar.

iiSeymour commented 1 year ago

https://github.com/nanoporetech/bonito/commit/8c96eb894a9cbdd917c9797d8a4f5531c1dcb935 makes sample_id optional.