artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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Error running artic minion #96

Open jvelasquez24 opened 2 years ago

jvelasquez24 commented 2 years ago

Hello I ran the following command artic minion --normalise 200 --threads 4 --scheme-directory ~/artic-ncov2019/primer_schemes --read-file artic.fastq --fast5-directory fast5_pass/ --sequencing-summary sequencing_summary.txt ncov2019/V4 artic_sample

and I get the following errors. I am not sure what would solve this issue. /Joseline/.conda/envs/joseline/lib/python3.9/site-packages/clint-0.5.1-py3.9.egg/clint/textui/prompt.py:68: SyntaxWarning: "is not" with a literal. Did you mean "!="? /Joseline/.conda/envs/joseline/lib/python3.9/site-packages/clint-0.5.1-py3.9.egg/clint/textui/prompt.py:68: SyntaxWarning: "is not" with a literal. Did you mean "!="? Traceback (most recent call last): File "/Joseline/.conda/envs/joseline/bin/artic", line 33, in sys.exit(load_entry_point('artic==1.2.1', 'console_scripts', 'artic')()) File "/Joseline/.conda/envs/joseline/lib/python3.9/site-packages/artic-1.2.1-py3.9.egg/artic/pipeline.py", line 222, in main args.func(parser, args) File "/Joseline/.conda/envs/joseline/lib/python3.9/site-packages/artic-1.2.1-py3.9.egg/artic/pipeline.py", line 20, in run_subtool from . import minion as submodule File "/Joseline/.conda/envs/joseline/lib/python3.9/site-packages/artic-1.2.1-py3.9.egg/artic/minion.py", line 10, in from .vcftagprimersites import read_bed_file File "/Joseline/.conda/envs/joseline/lib/python3.9/site-packages/artic-1.2.1-py3.9.egg/artic/vcftagprimersites.py", line 4, in import vcf File "/.conda/envs/joseline/lib/python3.9/site-packages/PyVCF-0.6.8-py3.9.egg/vcf/init.py", line 9, in from vcf.parser import Reader, Writer File "/Joseline/.conda/envs/joseline/lib/python3.9/site-packages/PyVCF-0.6.8-py3.9.egg/vcf/parser.py", line 25, in from model import _Call, _Record, make_calldata_tuple ModuleNotFoundError: No module named 'model'

Thanks in advance!