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artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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guppyplex not found #25

Closed splaisan closed 4 years ago

splaisan commented 4 years ago

Probably a stupid error of mine, I installed Artic from github a couple of weeks ago and try to run the tutorial from https://artic.network/ncov-2019/ncov2019-bioinformatics-sop.html on my ubuntu 16 server with guppy and ONT software present.

should I replace : artic guppyplex --min-length 400 --max-length 700 --directory output_directory/barcode03 --prefix run_name

by some other command?

Is my conda env outdated?

Thanks

artic -h
usage: artic [-h] [-v]
             {extract,basecaller,demultiplex,minion,gather,filter,rampart,run}
             ...

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         Installed Artic version

[sub-commands]:
  {extract,basecaller,demultiplex,minion,gather,filter,rampart,run}
    extract             Create an empty poredb database
    basecaller          Display basecallers in files
    demultiplex         Run demultiplex
    minion              Run demultiplex
    gather              Gather up demultiplexed files
    filter              Filter FASTQ files by length
    rampart             Interactive prompts to start RAMPART
    run                 Process an entire run folder interactively
(artic-ncov2019) u0002316@gbw-s-pacbio01:/data/covid19/multiplex_run8_24_pool5

$ artic -v
artic 1.0.0
splaisan commented 4 years ago

Thus I had an old version of artic although the reported version was 1.0.0 :-( reinstalled and gained the new function guppyplex

artic -h
usage: artic [-h] [-v]
             {extract,basecaller,demultiplex,minion,gather,guppyplex,filter,rampart,run}
             ...

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         Installed Artic version

[sub-commands]:
  {extract,basecaller,demultiplex,minion,gather,guppyplex,filter,rampart,run}
    extract             Create an empty poredb database
    basecaller          Display basecallers in files
    demultiplex         Run demultiplex
    minion              Run demultiplex
    gather              Gather up demultiplexed files
    guppyplex           Aggregate pre-demultiplexed reads from MinKNOW/Guppy
    filter              Filter FASTQ files by length
    rampart             Interactive prompts to start RAMPART
    run                 Process an entire run folder interactively

$ artic --version
artic 1.0.0