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artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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AssertionError: error: readgroup not found in provided primer scheme (1) #45

Open fabgenomics opened 3 years ago

fabgenomics commented 3 years ago

Hi, I'm testing the pipeline and everything goes well until : artic_plot_amplicon_depth --primerScheme /home/linux/programmes/artic-ncov2019/primer_schemes/ZaireEbola V1/ZaireEbola.scheme.bed --sampleID ebov-mayinga --outFilePrefix ebov-mayinga ebov-mayinga*.depths

Traceback (most recent call last): File "/home/linux/miniconda3/envs/artic-ncov2019/bin/artic_plot_amplicon_depth", line 10, in sys.exit(main()) File "/home/linux/miniconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/plot_amplicon_depth.py", line 143, in main go(args) File "/home/linux/miniconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/plot_amplicon_depth.py", line 76, in go rg)

AssertionError: error: readgroup not found in provided primer scheme (1)

Command failed:artic_plot_amplicon_depth --primerScheme /home/linux/programmes/artic-ncov2019/primer_schemes/ZaireEbola/V1/ZaireEbola.scheme.bed --sampleID ebov-mayinga --outFilePrefix ebov-mayinga ebov-mayinga*.depths

How can I solve this? Thk

will-rowe commented 3 years ago

Hi - can you let me know what version of the pipeline you are using please? (run artic --version)

fabgenomics commented 3 years ago

artic 1.1.3

will-rowe commented 3 years ago

Sorry about that - this is actually fixed in a pull request already and will hopefully be in master soon. It's because the readgroup in that primer scheme is an int and not a string.