Cano not import name "BadGzipFile"

[alienzj]

Hi, FOI-bioinformatics team member,

I meet error when i run:

flextaxd-create -db gtdb_r95.sqlite3 -o taxonomy/ --genomes_path gtdb/release95/fastani/database/ -p 20 --verbose -
-logs build_kraken2.db.log --create --db_name gtdb_k2_db --dbprogram kraken2

2020-11-13 10:42:07,494 create_databases [INFO ]  FlexTaxD-create logging initiated!
2020-11-13 10:42:07,531 create_databases [INFO ]  Processing files; create kraken seq.map
2020-11-13 10:42:07,532 DatabaseConnection [INFO ]  gtdb_r95.sqlite3 opened successfully.
2020-11-13 10:42:07,652 ProcessDirectory [INFO ]  Number of genomes annotated in database 31910
2020-11-13 10:42:07,652 ProcessDirectory [INFO ]  Process genome path (gtdb/release95/fastani/database/)
2020-11-13 10:42:08,306 ProcessDirectory [INFO ]  Processed 31910 genomes
2020-11-13 10:42:08,341 create_databases [INFO ]  Loading module: CreateKrakenDatabase
Traceback (most recent call last):
File "/ldfssz1/ST_META/share/User/zhujie/.conda/envs/bioenv/bin/flextaxd-create", line 10, in <module>
sys.exit(main())
File "/ldfssz1/ST_META/share/User/zhujie/.conda/envs/bioenv3.7/lib/python3.7/site-packages/flextaxd/create_databases.py", line 195, in main
classifier = dynamic_import("modules", "CreateKrakenDatabase")
File "/ldfssz1/ST_META/share/User/zhujie/.conda/envs/bioenv3.7/lib/python3.7/site-packages/flextaxd/create_databases.py", line 42, in dynamic_import
module = import_module(".".join([abs_module_path,class_name]))
File "/ldfssz1/ST_META/share/User/zhujie/.conda/envs/bioenv3.7/lib/python3.7/importlib/__init__.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1006, in _gcd_import
File "<frozen importlib._bootstrap>", line 983, in _find_and_load
File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 677, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 728, in exec_module
File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
File "/ldfssz1/ST_META/share/User/zhujie/.conda/envs/bioenv3.7/lib/python3.7/site-packages/flextaxd/modules/CreateKrakenDatabase.py", line 17, in <module>
from gzip import BadGzipFile
ImportError: cannot import name 'BadGzipFile' from 'gzip' (/ldfssz1/ST_META/share/User/zhujie/.conda/envs/bioenv3.7/lib/python3.7/gzip.py)

[davve2]

Hi thanks for reporting this issue!

This seems to occur using python 3.7 for some reason! The problem should not occur using python 3.8 (I just tested the two options), I will look for a solution using python 3.7, in the meantime I suggest to upgrade your python version in your conda environment

conda install python=3.8

/David

[davve2]

@alienzj I have implemented a solution and it will come with the next version (v0.3.5) until then please use python 3.8 or later!

[alienzj]

Thanks, I will try.