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The ARTIC field bioinformatics pipeline
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artic minion pyhton3.6 error #49

Closed shashibioinfo143 closed 3 years ago

shashibioinfo143 commented 4 years ago

Hi sir,

I have installed Miniconda Python 3.6 version, conda version 4.8.3. i got following error if you can please resolve this issue.

Thanks

artic minion --threads 8 --scheme-directory ~/artic-ncov2019/primer_schemes --read-file sample01.fastq --sequencing-summary /data/COVID_SET1/COVID-19/merged_fastq_files/ artic-ncov2019/primer_schemes/ nCoV-2019/V3 sample01

Traceback (most recent call last): File "/home/grid/miniconda3/envs/artic-ncov2019/bin/artic", line 10, in sys.exit(main()) File "/home/grid/miniconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/pipeline.py", line 216, in main args.func(parser, args) File "/home/grid/miniconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/pipeline.py", line 35, in run_subtool submodule.run(parser, args) File "/home/grid/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)

nickloman commented 4 years ago

The command has an extra argument artic-ncov2019/primer_schemes/ which should not be present, i.e. it should be:

artic minion --threads 8 --scheme-directory ~/artic-ncov2019/primer_schemes --read-file sample01.fastq --sequencing-summary /data/COVID_SET1/COVID-19/merged_fastq_files/ nCoV-2019/V3 sample01

nickloman commented 4 years ago

Additionally, unless you are using --medaka you will need to add the --fast5-directory argument, and the --sequencing-summaryshould point to a sequencing summary not a directory.

shashibioinfo143 commented 4 years ago

Thank you so much for response The issue is resolved. If you can let me know document of output results explanation from artic workflow

will-rowe commented 3 years ago

Hi @shashibioinfo143 - sorry for missing this.

You can find details on the output files in the SOP - I'll update the docs to give more details too.

Closing this issue now as the original problem is resolved.