fail to built kraken2_db by moshipit
I use the Docker image from Quay, When building the Kraken2 and Bracken databases, it always fails to download the files
. This command line seems to not support resumable downloads.
mosh annotate build-kraken-db \
--p-collection pluspf \
--p-use-ftp \
--p-threads 60 \
--o-kraken2-db ./cache:kraken2_db \
--o-bracken-db ./cache:bracken_db \
--use-cache /data/mydata/myProjects/meta/mymoshpit/cache \
--verbose
output like this
Found the latest "pluspf" database: kraken/k2_pluspf_20251015.tar.gz.
Downloading the "kraken/k2_pluspf_20251015.tar.gz" database: 72%|▋| 56.0G/77.5GTraceback (most recent call last):
File "/opt/conda/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/urllib3/response.py", line 779, in _error_catcher
yield
File "/opt/conda/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/urllib3/response.py", line 925, in _raw_read
raise IncompleteRead(self._fp_bytes_read, self.length_remaining)
urllib3.exceptions.IncompleteRead: IncompleteRead(60099215657 bytes read, 23110581710 more expected)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/requests/models.py", line 820, in generate
yield from self.raw.stream(chunk_size, decode_content=True)
File "/opt/conda/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/urllib3/response.py", line 1091, in stream
data = self.read(amt=amt, decode_content=decode_content)
File "/opt/conda/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/urllib3/response.py", line 1008, in read
data = self._raw_read(amt)
File "/opt/conda/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/urllib3/response.py", line 903, in _raw_read
with self._error_catcher():
File "/opt/conda/envs/qiime2-moshpit-2025.7/lib/python3.10/contextlib.py", line 153, in __exit__
self.gen.throw(typ, value, traceback)
File "/opt/conda/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/urllib3/response.py", line 803, in _error_catcher
raise ProtocolError(arg, e) from e
urllib3.exceptions.ProtocolError: ('Connection broken: IncompleteRead(60099215657 bytes read, 23110581710 more expected)', IncompleteRead(60099215657 bytes read, 23110581710 more expected))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/q2cli/commands.py", line 529, in __call__
results = self._execute_action(
File "/opt/conda/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/q2cli/commands.py", line 601, in _execute_action
results = action(**arguments)
File "<decorator-gen-665>", line 2, in build_kraken_db
File "/opt/conda/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/qiime2/sdk/action.py", line 221, in bound_callable
outputs = self._callable_executor_(
File "/opt/conda/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/qiime2/sdk/action.py", line 362, in _callable_executor_
output_views = self._callable(**view_args)
File "/opt/conda/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/q2_annotate/kraken2/database.py", line 331, in build_kraken_db
_fetch_prebuilt_dbs(bracken_db, kraken2_db, collection, tmp)
File "/opt/conda/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/q2_annotate/kraken2/database.py", line 270, in _fetch_prebuilt_dbs
_fetch_db_collection(collection=collection, tmp_dir=tmp)
File "/opt/conda/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/q2_annotate/kraken2/database.py", line 243, in _fetch_db_collection
for chunk in response.iter_content(chunk_size=CHUNK_SIZE):
File "/opt/conda/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/requests/models.py", line 822, in generate
raise ChunkedEncodingError(e)
requests.exceptions.ChunkedEncodingError: ('Connection broken: IncompleteRead(60099215657 bytes read, 23110581710 more expected)', IncompleteRead(60099215657 bytes read, 23110581710 more expected))
Plugin error from annotate:
('Connection broken: IncompleteRead(60099215657 bytes read, 23110581710 more expected)', IncompleteRead(60099215657 bytes read, 23110581710 more expected))
See above for debug info.
Downloading the "kraken/k2_pluspf_20251015.tar.gz" database: 72%|▋| 56.0G/77.5G
How to solve this problem?
How can I use the already downloaded database to locally build the cache: kraken2_db and bracken_db?