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novoalab / Nano-tRNAseq

Quantitative analysis of native tRNA populations using direct RNA nanopore sequencing (Lucas*, Pryszcz* et al., Nat Biotech 2023)
GNU General Public License v3.0
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MinKNOW version impatibility #5

Open shengqh opened 1 year ago

shengqh commented 1 year ago

Based on introduction, I updated the flow_cells.toml and copied the sequencing_MIN106_RNA_short.toml to /opt/ont/minknow/conf/package. However, my MinKNOW didn't recognize the sequencing_MIN106_RNA_short.toml with error message "Cannot be parsed correctly - MinKNOW version imcompatibility". My MinION is MC-114223 and MinKNOW version is 23.04.5 (bionic). There are a lot of difference between system sequencing_MIN106_RNA.toml and your sequencing_MIN106_RNA_short.toml. The system sequencing_MIN106_RNA.toml file attached. Would you please let me know how to modify the sequencing_MIN106_RNA_short.toml to make it compatible with my MinKNOW? Thank you so much.

minit@MC-114223:/opt/ont/minknow/conf/package/sequencing$ diff sequencing_MIN106_RNA.toml sequencing_MIN106_RNA_short.toml
10c10
< flow_cells = ["FLO-MIN106", "FLO-FLG001"]
---
> flow_cells = ["FLO-MIN106_short", "FLO-FLG001_short"]
19,22d18
< [meta.protocol.mk1c]
< default_basecall_model = "rna_r9.4.1_70bps_hac_mk1c.cfg"
< available_basecall_models = ["rna_r9.4.1_70bps_fast_mk1c.cfg", "rna_r9.4.1_70bps_hac_mk1c.cfg"]
<
28c24
< minknow_core = "5.5"
---
> minknow_core = "5.0"
51a48,50
> [basecaller_configuration.read_filtering]
> min_qscore = 7
>
88,89c87,88
<      "adapter=         (median_before,gt,160)&(median_before,lt,280)&(local_range,gt,5)&(local_range,lt,50)&(local_median,gt,50)&(local_median,lt,120)&(local_median_sd,gt,0.5)&(local_median_sd,lt,2.5)&(duration,lt,5)",
<      "strand=          (local_range,gt,25)&(local_range,lt,60)&(local_median,gt,60)&(local_median,lt,115)&(local_median_sd,gt,1)&(local_median_sd,lt,4)&(duration,gt,2)",
---
>      "adapter=         (median_before,gt,160)&(median_before,lt,280)&(local_range,gt,5)&(local_range,lt,50)&(local_median,gt,50)&(local_median,lt,120)&(local_median_sd,gt,0.5)&(local_median_sd,lt,2.5)&(duration,lt,2)",
>      "strand=          (local_range,gt,25)&(local_range,lt,60)&(local_median,gt,60)&(local_median,lt,115)&(local_median_sd,gt,1)&(local_median_sd,lt,4)&(duration,gt,1)",
125,126c124,126
< enable_relative_unblock_voltage = false
< effective_unblock_voltage = 110
---
> enable_relative_unblock_voltage = true
> unblock_voltage_gap = 480
> run_time = 172800 # (seconds) 1hr=3600
131a132,133
> #simulation="/path_to_bulk_dump.fast5"
>
183,184c185,186
< rest_duration  = [ 3, 3, 15, 30 ]
< repeats        = [ 1, 1, 4, 4 ]
---
> rest_duration  = [   3,   3,   15, 30   ]
> repeats        = [   1,   1,    4,  4   ]
224,227c226
< enabled = true
<
< interval = 7200 # Correct this often (seconds)
< reset_interval_every_mux_scan = true  # Only run every x seconds _inside_ a mux scan
---
> enabled = false
228a228
> interval = 5400 # Correct this often (seconds)
232,233d231
< minimum_voltage_adjustment = 5
<
270a269
> muxes = [1, 2, 3, 4]
296,297c295,296
< rest_duration  = [ 3, 3, 15, 30 ]
< repeats        = [ 1, 1, 4, 4 ]
---
> rest_duration  = [   3,   3,   15, 30   ]
> repeats        = [   1,   1,    4,  4   ]
328,329c327,328
< rest_duration  = [ 3, 3, 3, 3 ]
< repeats        = [ 1, 1, 4, 4 ]
---
> rest_duration  = [   3,   3,   3, 3   ]
> repeats        = [   1,   1,    4,  4   ]
348,364c347
< arguments = ["--guppy_config=rna_r9.4.1_70bps_fast.cfg", "--enrich_unblock_min_sequence_length=200", "--deplete_stop_receiving_min_sequence_length=4000"]
<
< [custom_processes.read_until.mk1c]
< arguments = ["--guppy_config=rna_r9.4.1_70bps_fast_mk1c.cfg", "--enrich_unblock_min_sequence_length=200", "--deplete_stop_receiving_min_sequence_length=4000"]
<
<
< ##################
< #   Run Until   #
< ##################
<
< [custom_processes.run_until]
< script = "sequencing/run_until/run_until_script.py"
< enabled = true
<
< # See the run until script argparse for parameters to pass
< # Anything passed by the UI will be on the end of this
< arguments = []
---
> arguments = ["--guppy_config=rna_r9.4.1_70bps_fast.cfg"]

sequencing_MIN106_RNA.toml.txt

lpryszcz commented 1 year ago

Hi @shengqh , the config files are compatible with MinKNOW v22.03 and likely also with v22.05 (info here https://github.com/novoalab/Nano-tRNAseq/releases).

In order to make it compatible with newer versions, you'll need to copy the default config sequencing_MIN106_RNA.toml as sequencing_MIN106_RNA_short.toml and change 3 lines:

Please create pull request with new config files stating which MinKNOW version they are compatible with.

Hope it helps, Leszek

vetmohit89 commented 5 months ago

I am also having similar issues. Can you please upgrade both the files for current minKnow version.

lpryszcz commented 5 months ago

Hi @vetmohit89 , I'm not going to upgrade the config. You can generate config compatible with your version of MinKNOW by following instructions above. I'll leave this issue open for visibility.