Resuming a run

[chocotwig]

Hi,

I am wondering -- if bonito terminates for whatsoever reason during a run, is there a way to restart the run and pick up from where it left off?

Thanks!

[iiSeymour]

I can think of a couple of ways to do this - but perhaps the providing a --skip flag that takes a file containing read_ids would be best? Then you could either use a new output file with > or append to the prior one with >>.

$ bonito basecaller  --half --skip read_ids dna_r9.4.1 reads >> call.fasta 

Does that work for you?

[cdebuck]

Hi,

I am using bonito version 0.5.1 and I'm also interested in restarting a run, and supplying read-ids that bonito can skip. I looked into the --skip argument, but I cannot use it in the way that is described above, because I cannot supply a file with read_ids to the --skip argument.
Is this a bug, or am I misunderstanding the use of the --skip argument?

[iiSeymour]

Hi @cdebuck - sorry, it wasn't implemented exactly as described here. You can supply a file of read ids with the --read-id option and add --skip to change the behaviour to skip the reads instead of basecall only those reads.

$ head rid
f39c764f-0028-4de5-b5e6-06d674dfd260
ff7a4c88-caa8-41e8-9e03-501f3e3e7700
b6dd8879-cdef-41a6-94ca-bdb28be28111
190c4078-17b0-4d07-aec7-113c23e5ce27
540ced5c-fcf2-4375-8a36-69e28a4c7e74
$  bonito basecaller $model $fast5s --skip --read-ids rid  > calls.bam