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artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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Help with vcf_merge #99

Closed chodarq closed 2 years ago

chodarq commented 2 years ago

Hello. I have been using the pipeline with no problems for the past few months, but today I had a glitch:

Traceback (most recent call last): File "/home/chodar/miniconda3/envs/artic-ncov2019/bin/artic_vcf_merge", line 10, in <module> sys.exit(main()) File "/home/chodar/miniconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/vcf_merge.py", line 55, in main vcf_merge(args) File "/home/chodar/miniconda3/envs/artic-ncov2019/lib/python3.6/site-packages/artic/vcf_merge.py", line 26, in vcf_merge vcf_reader.infos["Pool"] = vcf.parser._Format("Pool", 1, "String", "The pool name") TypeError: __new__() missing 1 required positional argument: 'type_code'

First I thought it might be something associated with my reads, but then I tried an assembly with some sequences I had successfully used before, but the error was the same.

Does it happen to anyone else? Thanks.

chodarq commented 2 years ago

Well. Reinstall environment correct the error. Bye.