Please read the following before posting!
This is related to installation errors in diamond database and eggnog database
But now we have the same problem in Moshpit version 2026.1, annotate fetch-eggnog-db
The plugin wants to download http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog.taxa.tar.gz but in reality this file is here: http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog.db.gz
Command and output:
mosh annotate fetch-eggnog-db \
--o-db eggnog_db.qza \
--verbose
Output:
import pkg_resources
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: download_eggnog_data.py -y -D --data_dir /tmp/qiime2/user/processes/8091-1774988190.54@user/tmp/q2-OutPath-8397_eb5
Downloading "eggnog.db" at /tmp/qiime2/user/processes/8091-1774988190.54@user/tmp/q2-OutPath-8397_eb5...
cd /tmp/qiime2/user/processes/8091-1774988190.54@user/tmp/q2-OutPath-8397_eb5 && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O eggnog.db.gz http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog.db.gz && echo Decompressing... && gunzip eggnog.db.gz
--2026-03-31 22:17:25-- http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog.db.gz
Resolving eggnogdb.embl.de (eggnogdb.embl.de)... 194.94.44.170
Connecting to eggnogdb.embl.de (eggnogdb.embl.de)|194.94.44.170|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2026-03-31 22:17:25 ERROR 404: Not Found.
Downloading "eggnog.taxa.db" at /tmp/qiime2/user/processes/8091-1774988190.54@user/tmp/q2-OutPath-8397_eb5...
cd /tmp/qiime2/user/processes/8091-1774988190.54@user/tmp/q2-OutPath-8397_eb5 && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O eggnog.taxa.tar.gz http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog.taxa.tar.gz && echo Decompressing... && tar -zxf eggnog.taxa.tar.gz && rm eggnog.taxa.tar.gz
--2026-03-31 22:17:25-- http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog.taxa.tar.gz
Resolving eggnogdb.embl.de (eggnogdb.embl.de)... 194.94.44.170
Connecting to eggnogdb.embl.de (eggnogdb.embl.de)|194.94.44.170|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2026-03-31 22:17:25 ERROR 404: Not Found.
Skipping diamond database (or already present). Use -f to force download
Skipping novel families diamond and annotation databases (or already present). Use -F and -f to force download
Skipping Pfam database (or already present). Use -P and -f to force download
Skipping MMseqs2 database (or already present). Use -M and -f to force download
No HMMER database requested. Use "-H -d taxid" to download the hmmer database for taxid
Finished.
Traceback (most recent call last):
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/q2cli/commands.py", line 573, in __call__
results = self._execute_action(
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/q2cli/commands.py", line 645, in _execute_action
results = action(**arguments)
File "<decorator-gen-1007>", line 2, in fetch_eggnog_db
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/rachis/sdk/action.py", line 307, in bound_callable
outputs = self._callable_executor_(
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/rachis/sdk/action.py", line 513, in _callable_executor_
self.signature.coerce_given_outputs(output_views, output_types,
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/rachis/core/type/signature.py", line 509, in coerce_given_outputs
output = self._create_output_artifact(
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/rachis/core/type/signature.py", line 531, in _create_output_artifact
artifact = rachis.sdk.Artifact._from_view(
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/rachis/sdk/result.py", line 704, in _from_view
result = transformation(view, validate_level)
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/rachis/core/transform.py", line 68, in transformation
self.validate(view, level=validate_level)
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/rachis/core/transform.py", line 143, in validate
view.validate(level)
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/rachis/plugin/model/directory_format.py", line 183, in validate
raise ValidationError("Unrecognized file (%s) for %s."
rachis.core.exceptions.ValidationError: Unrecognized file (/tmp/qiime2/user/processes/8091-1774988190.54@user/tmp/q2-OutPath-8397_eb5/eggnog.taxa.tar.gz) for EggnogRefDirFmt.
Plugin error from annotate:
Unrecognized file (/tmp/qiime2/user/processes/8091-1774988190.54@user/tmp/q2-OutPath-8397_eb5/eggnog.taxa.tar.gz) for EggnogRefDirFmt.
See above for debug info.
(qiime2-moshpit-2026.1) user@I2510:/media/data$ mosh annotate fetch-eggnog-db --o-db eggnog_db.qza --verbose
/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/q2_assembly/_utils.py:14: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
Running external command line application(s). This may print messages to stdout and/or stderr.
The command(s) being run are below. These commands cannot be manually re-run as they will depend on temporary files that no longer exist.
Command: download_eggnog_data.py -y -D --data_dir /tmp/qiime2/user/processes/8305-1774988878.91@user/tmp/q2-OutPath-aqbw8q6j
Downloading "eggnog.db" at /tmp/qiime2/user/processes/8305-1774988878.91@user/tmp/q2-OutPath-aqbw8q6j...
cd /tmp/qiime2/user/processes/8305-1774988878.91@user/tmp/q2-OutPath-aqbw8q6j && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O eggnog.db.gz http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog.db.gz && echo Decompressing... && gunzip eggnog.db.gz
--2026-03-31 22:28:33-- http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog.db.gz
Resolving eggnogdb.embl.de (eggnogdb.embl.de)... 194.94.44.170
Connecting to eggnogdb.embl.de (eggnogdb.embl.de)|194.94.44.170|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2026-03-31 22:28:33 ERROR 404: Not Found.
Downloading "eggnog.taxa.db" at /tmp/qiime2/user/processes/8305-1774988878.91@user/tmp/q2-OutPath-aqbw8q6j...
cd /tmp/qiime2/user/processes/8305-1774988878.91@user/tmp/q2-OutPath-aqbw8q6j && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O eggnog.taxa.tar.gz http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog.taxa.tar.gz && echo Decompressing... && tar -zxf eggnog.taxa.tar.gz && rm eggnog.taxa.tar.gz
--2026-03-31 22:28:33-- http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog.taxa.tar.gz
Resolving eggnogdb.embl.de (eggnogdb.embl.de)... 194.94.44.170
Connecting to eggnogdb.embl.de (eggnogdb.embl.de)|194.94.44.170|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2026-03-31 22:28:33 ERROR 404: Not Found.
Skipping diamond database (or already present). Use -f to force download
Skipping novel families diamond and annotation databases (or already present). Use -F and -f to force download
Skipping Pfam database (or already present). Use -P and -f to force download
Skipping MMseqs2 database (or already present). Use -M and -f to force download
No HMMER database requested. Use "-H -d taxid" to download the hmmer database for taxid
Finished.
Traceback (most recent call last):
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/q2cli/commands.py", line 573, in __call__
results = self._execute_action(
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/q2cli/commands.py", line 645, in _execute_action
results = action(**arguments)
File "<decorator-gen-1007>", line 2, in fetch_eggnog_db
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/rachis/sdk/action.py", line 307, in bound_callable
outputs = self._callable_executor_(
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/rachis/sdk/action.py", line 513, in _callable_executor_
self.signature.coerce_given_outputs(output_views, output_types,
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/rachis/core/type/signature.py", line 509, in coerce_given_outputs
output = self._create_output_artifact(
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/rachis/core/type/signature.py", line 531, in _create_output_artifact
artifact = rachis.sdk.Artifact._from_view(
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/rachis/sdk/result.py", line 704, in _from_view
result = transformation(view, validate_level)
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/rachis/core/transform.py", line 68, in transformation
self.validate(view, level=validate_level)
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/rachis/core/transform.py", line 143, in validate
view.validate(level)
File "/opt/miniconda3/envs/qiime2-moshpit-2026.1/lib/python3.10/site-packages/rachis/plugin/model/directory_format.py", line 183, in validate
raise ValidationError("Unrecognized file (%s) for %s."
rachis.core.exceptions.ValidationError: Unrecognized file (/tmp/qiime2/user/processes/8305-1774988878.91@user/tmp/q2-OutPath-aqbw8q6j/eggnog.taxa.tar.gz) for EggnogRefDirFmt.
Plugin error from annotate:
Unrecognized file (/tmp/qiime2/user/processes/8305-1774988878.91@user/tmp/q2-OutPath-aqbw8q6j/eggnog.taxa.tar.gz) for EggnogRefDirFmt.
See above for debug info.
Can’t I edit download_eggnog_data.py?