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nanoporetech / minknow_api

Protobuf and gRPC specifications for the MinKNOW API
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start_protocol.py - argument experiment-duration acccepted but not used downstream #20

Closed neuropathbasel closed 3 years ago

neuropathbasel commented 3 years ago

I tried to reduce the runtime from your example from 24 hrs to 1 hour. In suitable python environment I do run: $ python start_protocol.py \

--host localhost --position MN32621 \ --sample-id "2021_04_28b_cmd_run_01" \ --experiment-group "2021_04_28b_cmd_run_01" \ --experiment-duration 1 \ --basecalling \ --fastq --bam \ --verbose \ --kit SQK-RBK004 \ --barcoding \ --barcode-kits "SQK-RBK004"

but in the started protocols I do find the default runtime of 72 hours: <...> Starting protocol on 1 positions Starting protocol sequencing/sequencing_MIN106_DNA:FLO-MIN106:SQK-RBK004 on position MN32621 DEBUG:minknow_api.tools.protocols:Built protocol arguments: --base_calling=on --barcoding barcoding_kits=['SQK-RBK004',] --experiment_time=72 --fast5=off --fastq=on --fastq_data compress --fastq_reads_per_file=4000 --bam=on --active_channel_selection=on --mux_scan_period=1.5 Started protocol e39a452b-ee3e-49af-8d68-39d9b0b0f9dc

How can I correct this?

Thanks Claus

0x55555555 commented 3 years ago

Hello @neuropathbasel,

There was an issue with the example code which we had fixed in the upcoming release.

I've backported it and tagged 4.2.4 - please try this release.

neuropathbasel commented 3 years ago

Hi George, Many thanks. this works. I highly appreciate your rapid support. Claus

0x55555555 commented 3 years ago

No worries - let us know if you hit further issues!