Closed shair89 closed 1 month ago
Hmm - this is a little concerning - you are correct that it looks as though it is working, but if you are not seeing unblocked reads in the minKNOW GUI something is wrong.
Are you running on a bulk file or a live run?
We will do some more testing here - our minknow 6.0 branch isn't technically live yet but it should work!
Just as a sanity check - if you are running playback - could you try:
targets = ["chr21"]
and not:
targets = "chr21"
I have tried it on a playback bulk file and on a live sequencing run - both with the same results unfortunately!
I've tried changing the targets (including pointing to a BED file) and it hasn't changed the outcome.
Very confused as the basecalling and mapping does seem to be working behind the scenes - just doesn't then reject the reads it should be.
OK - my apologies for the issues.
Would you be able to share the log file from the run with us?
From a very short test run of a few minutes - readfish_targets.log
OK - we think we've identified a bug - will push a fix but please don't try running again on this branch till this is fixed.
Hi @shair89 - this is fixed in main, and we will do a release to PyPI this week.
Hi,
I am running with readfish/minknow6-compatibility alongside Minknow 6.0.8 on a MinION Mk1B.
Everything appears to be working and
unblock-all
works exactly as expected with a nice peak ~400bp.However when using
readfish targets
I get no rejected reads on the Minknow histogram despite the TOML file validating OK and it producing both a log file and a tsv file containing reads which have the decision "unblock". It is also able to output the live.fq and live.paf for the "rejected reads" which look correct - I have double checked andcontrol = false
in the TOML and--dry-run = false
on the command line. It seems like the unblock decisions are not being fed back to MinKnow?I have tried with a few different targets options in the TOML file, all with the same result.
command:
readfish targets --device MNXXXX --log-file readfish_logs.log --toml readfish.toml --experiment-name "test"
TOML:
Example of log as it's "working":
Hopefully I'm doing something simple wrong but any advice would be appreciated!
Thanks, Steven