ModuleNotFoundError: No module named 'mongoengine'
AmirHoseinSafari opened this issue · 2 comments
Hi,
I hope all is well.
I am getting the "ModuleNotFoundError: No module named 'mongoengine'" error while I am using Mykrobe.
Here is the log:
1_ conda install -c bioconda mykrobe
2_ wget -O test_reads.fq.gz https://ndownloader.figshare.com/files/21059229
3_ mykrobe predict SAMPLE tb --output out.json --format json --seq test_reads.fq.gz
Traceback (most recent call last):
File "/home/ahsafari/miniconda3/envs/pytorch_env/bin/mykrobe", line 11, in
sys.exit(main())
File "/home/ahsafari/miniconda3/envs/pytorch_env/lib/python3.7/site-packages/mykrobe/cli.py", line 8, in main
args.func(parser, args)
File "/home/ahsafari/miniconda3/envs/pytorch_env/lib/python3.7/site-packages/mykrobe/parser.py", line 29, in run_subtool
from mykrobe.cmds.amr import run
File "/home/ahsafari/miniconda3/envs/pytorch_env/lib/python3.7/site-packages/mykrobe/cmds/amr.py", line 14, in
from mykrobe.typing import CoverageParser
File "/home/ahsafari/miniconda3/envs/pytorch_env/lib/python3.7/site-packages/mykrobe/typing/init.py", line 5, in
from mykrobe.typing.typer.presence import PresenceTyper
File "/home/ahsafari/miniconda3/envs/pytorch_env/lib/python3.7/site-packages/mykrobe/typing/typer/presence.py", line 3, in
from mykrobe.variants.schema.models import SequenceCall
File "/home/ahsafari/miniconda3/envs/pytorch_env/lib/python3.7/site-packages/mykrobe/variants/init.py", line 1, in
from mykrobe.variants.schema.models import VariantCallSet
File "/home/ahsafari/miniconda3/envs/pytorch_env/lib/python3.7/site-packages/mykrobe/variants/schema/models/init.py", line 1, in
from mykrobe.variants.schema.models.variants import Variant
File "/home/ahsafari/miniconda3/envs/pytorch_env/lib/python3.7/site-packages/mykrobe/variants/schema/models/variants.py", line 4, in
from mongoengine import Document
ModuleNotFoundError: No module named 'mongoengine'
What is the version of mykrobe in your conda environment? mykrobe --version
Closing due to no response. Please reopen if you still experience this issue with the latest version.