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artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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NameError: name 'barcode_directory' is not defined #29

Closed MaestSi closed 4 years ago

MaestSi commented 4 years ago

Hi, I tried the new version of the pipeline on SP1 data, as I saw there had been some updates. However, the first command for artic guppyplex: artic guppyplex --min-length 400 --max-length 700 --directory basecalling/ --prefix SP1 Fails with error:

Traceback (most recent call last):
  File "/home/simone/miniconda3/envs/artic-ncov2019/bin/artic", line 8, in <module>
    sys.exit(main())
  File "/home/simone/miniconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/pipeline.py", line 216, in main
    args.func(parser, args)
  File "/home/simone/miniconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/pipeline.py", line 35, in run_subtool
    submodule.run(parser, args)
  File "/home/simone/miniconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/guppyplex.py", line 36, in run
    fastq_outfn = "%s_%s.fastq" % (args.prefix, os.path.basename(barcode_directory))
NameError: name 'barcode_directory' is not defined

Are there any issues in the command I am using? Thanks in advance, Simone

nickloman commented 4 years ago

Many thanks for the bug report, it should be fixed now.

MaestSi commented 4 years ago

Unfortunately I keep having the same issue after repeating installation. Probably some time is needed for changes to take effect. Ok, I just saw the pull request in the fieldbioinformatics page is still open. Thanks.

nickloman commented 4 years ago

Apologies, I hadn't merged the pull request yet. Please try again?

MaestSi commented 4 years ago

I confirm it now works, thanks! Simone