Error when running the MinION pipeline command.

[GeorgiM26]

Hello, Whenever i am running the minION pipeline command I run into an error which I am unable to decipher and, hence, troubleshoot. In the following, please find the exact error I am getting:

Command Used:

artic minion --normalise 200 --scheme-directory ~/artic-ncov2019/primer_schemes/ --read-file Aug24_sample1.fastq --fast5-directory ../../../fast5_skip/ --sequencing-summary ../../../Basecalling_skipped/sequencing_summary.txt ~/artic-ncov2019/primer_schemes/nCoV-2019/V3/ Sample1

Error message:

Traceback (most recent call last): File "/home/bio/miniconda3/envs/artic-ncov2019/bin/artic", line 10, in sys.exit(main()) File "/home/bio/miniconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/pipeline.py", line 216, in main args.func(parser, args) File "/home/bio/miniconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/pipeline.py", line 35, in run_subtool submodule.run(parser, args) File "/home/bio/miniconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/minion.py", line 23, in run scheme_name, scheme_version = args.scheme.split('/') ValueError: too many values to unpack (expected 2)

N.B: Please note that the artic environment was getting stuck at solving environment with the 64-bit python 3.6 version of miniconda. Therefore it was installed via the latest version of miniconda3 (with Py3.8). I am unsure if this is contributing to the error. Also, please do excuse the hectic directory arrangement in the command.

Thank you very much. Sincerely, Georgi Merhi.

[nickloman]

The last part of the command should read:

nCoV-2019/V3 Sample1

rather than:

~/artic-ncov2019/primer_schemes/nCoV-2019/V3/ Sample1

[GeorgiM26]

Thank you Professor Loman, everything ran perfectly!