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'
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!