start_protocol.py Error with --barcoding option #72
Description
I am trying to start a run on Minion with Flongle adapter using the API. I am starting with the start_protcol.py example script. I call the script with the following params.
python3 start_protocol.py --host localhost --position MN45321 --sample-id "my_sample" --experiment-group "my_group" --experiment-duration 24 --kit SQK-RPB114-24 --basecalling --fastq --barcoding --product-code FLO-FLG114
And I get output:
Starting protocol on 1 positions
Started protocol:
run_id=a0ab180e-f713-4a84-a671-273bba8dc0e7
position=MN45321
flow_cell_id=
user_specified_flow_cell_id=
Within the MinKnow Software I see an error immediately.
Script failed. Please check for error messages below or restart the experiment. If the problem persists please contact support.
There are no other error messages in the System Messages. I found a control server log at C:\data\logs\MN45321
In that log I see the following:
2025-04-08 08:46:29.814848 ERROR: script_crashed (script)
exit_code: 2
run_id: a0ab180e-f713-4a84-a671-273bba8dc0e7
script_output: C:\Program Files\OxfordNanopore\MinKNOW\conf\package\sequencing/run_until/run_until_script.py:13: DeprecationWarning:
Pyarrow will become a required dependency of pandas in the next major release of pandas (pandas 3.0),
(to allow more performant data types, such as the Arrow string type, and better interoperability with other libraries)
but was not found to be installed on your system.
If this would cause problems for you,
please provide us feedback at pandas-dev/pandas#54466
import pandas as pd
usage: sequencing.py [-h] [--config CONFIG] [--sawtooth_url SAWTOOTH_URL]
[--bias_voltage_offset_lookup_server BIAS_VOLTAGE_OFFSET_LOOKUP_SERVER]
[--pore_type_check [PORE_TYPE_CHECK ...]]
[--disable_pore_check] [--department DEPARTMENT]
[--experiment_type EXPERIMENT_TYPE]
[--flow_cell_id FLOW_CELL_ID]
[--experiment_time EXPERIMENT_TIME]
[--start_bias_voltage START_BIAS_VOLTAGE]
[--base_calling {on,off}]
[--barcoding_kits BARCODING_KITS [BARCODING_KITS ...]]
[--trim_barcodes {on,off}]
[--barcoding BARCODING [BARCODING ...]]
[--alignment ALIGNMENT [ALIGNMENT ...]]
[--read_splitting READ_SPLITTING [READ_SPLITTING ...]]
[--bam {on,off}] [--fast5 {on,off}]
[--fast5_data {fastq,raw,trace_table,move_table,zlib_compress,vbz_compress} [{fastq,raw,trace_table,move_table,zlib_compress,vbz_compress} ...]]
[--pod5 {on,off}]
[--fastq_data {compress} [{compress} ...]]
[--bam_only_write_primary_alignment {on,off}]
[--bam_reads_per_file BAM_READS_PER_FILE | --bam_bases_per_batch BAM_BASES_PER_BATCH | --bam_disable_output_based_batching {on,off}]
[--bam_batch_duration BAM_BATCH_DURATION]
[--fast5_reads_per_file FAST5_READS_PER_FILE | --fast5_bases_per_batch FAST5_BASES_PER_BATCH | --fast5_disable_output_based_batching {on,off}]
[--fast5_batch_duration FAST5_BATCH_DURATION]
[--pod5_reads_per_file POD5_READS_PER_FILE | --pod5_bases_per_batch POD5_BASES_PER_BATCH | --pod5_disable_output_based_batching {on,off}]
[--pod5_batch_duration POD5_BATCH_DURATION]
[--split_files_by_barcode {on,off}]
[--split_pod5_files_by_barcode {on,off}]
[--fast5_reads_per_folder FAST5_READS_PER_FOLDER]
[--fastq {on,off}]
[--fastq_reads_per_file FASTQ_READS_PER_FILE | --fastq_bases_per_batch FASTQ_BASES_PER_BATCH | --fastq_disable_output_based_batching {on,off}]
[--fastq_batch_duration FASTQ_BATCH_DURATION]
[--generate_bulk_file {on,off}]
[--bulk_file_content BULK_FILE_CONTENT [BULK_FILE_CONTENT ...]]
[--read_filtering READ_FILTERING [READ_FILTERING ...]]
[--filter_unaligned {on,off}]
[--min_read_length {20,200,1000}]
[--skip_rejected_reads {on,off}]
[--mux_scan_period MUX_SCAN_PERIOD]
[--active_channel_selection {on,off}]
[--group_change_period GROUP_CHANGE_PERIOD]
[--basecaller_filename BASECALLER_FILENAME] [--kit KIT]
[--lamp_kit LAMP_KIT] [--pore_reserve {on,off}]
[--keep_power_on KEEP_POWER_ON] [--simulation SIMULATION]
sequencing.py: error: argument --barcoding: expected at least one argument
script_path: sequencing/sequencing_MIN114_DNA_e8_2_400K:FLO-FLG114:SQK-RPB114-24:400
2025-04-08 08:46:29.824199 INFO: protocol_finished_script_failure (script)
error: ExitCode=2
run_id: a0ab180e-f713-4a84-a671-273bba8dc0e7
2025-04-08 08:46:29.825048 INFO: sending_telemetry_message (ping)
data: {"acquisitions":[],"monitor":"protocol_end","script_name":"sequencing/sequencing_MIN114_DNA_e8_2_400K:FLO-FLG114:SQK-RPB114-24:400","stop_reason":"...
2025-04-08 08:46:29.825048 INFO: clear_request_for_disabling_OS_standby (util)
the --barcoding option in the start_protocol.py script is just a bool so I am not sure what I am missing here to make this work.