mattloose

I can't decide if it's better to cat the sequence_summary.txt files rather than keeping multiple versions. It's useful to parse info from there whilst basecalling is happening. Cumulative stats can...

To be honest - I think this stuff is best handled in the loop used to call these scripts rather than in the script itself?

Just bumping this again - after another crash where it's taken bonito nearly a day to just preprocess the reads...

So its the same error as before: Traceback (most recent call last): File "/usr/lib/python3.8/threading.py", line 932, in _bootstrap_inner self.run() File "/usr/local/lib/python3.8/dist-packages/ont_bonito_cuda11.3.0-0.5.1-py3.8.egg/bonito/multiprocessing.py", line 110, in run for item in self.iterator: File...

Just to update - I tried calling the same read set without using remora models and it crashes in the same way.

Good point - I will look at this asap. The folder number are simply batches of reads. However I am not sure this will run correctly on R9.4 and minknow...

Yes - just to confirm. Switching the mode to recursive won't be sufficient to fix. However there are other issues with read until at this moment in time (beyond these...

Actually - my comment above is incorrect. Switching the mode to recursive will fix it, but aReadUntil ignores reads that are already written to disk when you start running it....

Hi This version of the scripts no longer works with the current Ont api. You should refer to the latest apis from Nanopore. Thanks Matt Sent from my iPhone On...

As an additional point - I'd rather the runID in the fastq was maintained going forwards as a consistent identifier and not that the fastq was modified to match the...