installation errors in diamond database and eggnog database

Technical Support
1

The specific error information as follows:

qiime annotate fetch-diamond-db
--o-db /media/admin1/Database/database-cache:diamond_db
--verbose
/home/admin1/miniconda3/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/rescript/evaluate.py:25: UserWarning: pkg_resources is deprecated as an API. See Package Discovery and Resource Access using pkg_resources - setuptools 80.9.0 documentation . 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
Starting download...
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: wget -e robots=off -O /tmp/qiime2/admin1/processes/91767-1759806318.51@admin1/tmp/q2-OutPath-2vck626y/ref_db.dmnd.gz http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog_proteins.dmnd.gz

--2025-10-07 11:05:50-- http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog_proteins.dmnd.gz
Connecting to 127.0.0.1:7890... connected.
Proxy request sent, awaiting response... 404 Not Found
2025-10-07 11:05:51 ERROR 404: Not Found.

Traceback (most recent call last):
File "/home/admin1/miniconda3/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/q2cli/commands.py", line 529, in call
results = self._execute_action(
File "/home/admin1/miniconda3/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/q2cli/commands.py", line 601, in _execute_action
results = action(**arguments)
File "", line 2, in fetch_diamond_db
File "/home/admin1/miniconda3/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/qiime2/sdk/action.py", line 221, in bound_callable
outputs = self.callable_executor(
File "/home/admin1/miniconda3/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 "/home/admin1/miniconda3/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/q2_annotate/eggnog/dbs.py", line 127, in fetch_diamond_db
run_command(
File "/home/admin1/miniconda3/envs/qiime2-moshpit-2025.7/lib/python3.10/site-packages/q2_annotate/_utils.py", line 45, in run_command
subprocess.run(cmd, check=True, **kwargs)
File "/home/admin1/miniconda3/envs/qiime2-moshpit-2025.7/lib/python3.10/subprocess.py", line 526, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['wget', '-e', 'robots=off', '-O', '/tmp/qiime2/admin1/processes/91767-1759806318.51@admin1/tmp/q2-OutPath-2vck626y/ref_db.dmnd.gz', 'http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog_proteins.dmnd.gz']' returned non-zero exit status 8.

Plugin error from annotate:

Command '['wget', '-e', 'robots=off', '-O', '/tmp/qiime2/admin1/processes/91767-1759806318.51@admin1/tmp/q2-OutPath-2vck626y/ref_db.dmnd.gz', 'http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog_proteins.dmnd.gz']' returned non-zero exit status 8.

See above for debug info.

2

Hello @yawei,

The base URL http://eggnogdb.embl.de/ is currently leading me to this page

image
image1677Ɨ836 54.8 KB

And the URL to the actual .gz file is indeed a 404. It looks like the server the database is hosted on is currently down. We do not run this server.

I'm assuming, based on the fact that we even get this Nginx page, this site is still supposed to exist. Does anyone have more information about this?

1 Like
3

Based on a quick google, maybe they are moving the domains but DNS is slow?

Maybe this subdomain instead?

The names and folders match but I have no idea if they are the same!

4

I also found that site, but my computer doesn't trust it at all lol.

image

You're probably correct, though.

7

I also found that site, and I think they are indeed moving their domains. Can you provide me the underlying code of the fetch-diamond-db and fetch-eggnog-db commands, so that I can replace with the new domain name? Or could you develop a parameter that is stored in the cache using the local document? I also attempted to store this database using the "store-cache" command, but this database contains many files and I'm not quite sure if it will work well.

1 Like
8

It's in this repo and it looks like this may have already been fixed!

1 Like
9

Thanks for your kind reply.

It seems that I will have to wait until the release of version 2025.10 before I can use it.:grinning_face:

1 Like
10

Hi @yawei ,

The 2025.10 release will not be a long wait! But the other option is to try to install a development version of MOSHPIT to use the latest version, see here for instructions (warning: this is not the stable release so we cannot guarantee anything :wink: ):

2 Likes
12

Helloļ¼Œ the URL is still not update when I am runing fetch-eggnog-db command, although the fetch-diamond-db command is good, please fix this bug! thank you in advance~

13

Hi @yawei ,

Thank you for confirming that the fetch-diamond-db issue is now solved for you!

Now you mention a new issue with a different action, so could you please open a separate topic for this? In that topic, please post (1) your command, (2) the full error message and (3) version information or confirm that you are running version 2025.10?

Thanks!

14

Hello, Thanks for your replyļ¼

Actually, they are the same issue despite using a different action. The fetch-diamond-db action and fetch-eggnog-db action are using the same database URL.

I am running version 2025.10, please do not repair the bug until the next version, thanks very muchļ¼

sincerely~

15

Hi @yawei, thanks for confirming the Qiime version youā€™re running. They both share the same domain but the code has to be updated for each action individually. I only encountered the first issue, hence why it has only been updated in one place.

Iā€™m not sure what you mean by ā€œplease do not repair the bug until the next versionā€. Iā€™d be happy to update the URL across all actions otherwise.

1 Like
16

The specific error information as follows:

(qiime2-moshpit-2025.10) admin1@admin1-Default-string:~$ qiime annotate fetch-eggnog-db
--o-db /media/admin1/Database/database-cache:eggnog_db
--verbose
/home/admin1/miniconda3/envs/qiime2-moshpit-2025.10/lib/python3.10/site-packages/unifrac/init.py:9: UserWarning: pkg_resources is deprecated as an API. See Package Discovery and Resource Access using pkg_resources - setuptools 80.9.0 documentation . 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/admin1/processes/60908-1762251494.91@admin1/tmp/q2-OutPath-qfrjs41x

Downloading "eggnog.db" at /tmp/qiime2/admin1/processes/60908-1762251494.91@admin1/tmp/q2-OutPath-qfrjs41x...
cd /tmp/qiime2/admin1/processes/60908-1762251494.91@admin1/tmp/q2-OutPath-qfrjs41x && 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
--2025-11-04 18:18:49-- http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog.db.gz
Connecting to 127.0.0.1:7890... connected.
Proxy request sent, awaiting response... 404 Not Found
2025-11-04 18:18:49 ERROR 404: Not Found.

Downloading "eggnog.taxa.db" at /tmp/qiime2/admin1/processes/60908-1762251494.91@admin1/tmp/q2-OutPath-qfrjs41x...
cd /tmp/qiime2/admin1/processes/60908-1762251494.91@admin1/tmp/q2-OutPath-qfrjs41x && 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
--2025-11-04 18:18:49-- http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog.taxa.tar.gz
Connecting to 127.0.0.1:7890... connected.
Proxy request sent, awaiting response... 404 Not Found
2025-11-04 18:18:50 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 "/home/admin1/miniconda3/envs/qiime2-moshpit-2025.10/lib/python3.10/site-packages/q2cli/commands.py", line 567, in call
results = self._execute_action(
File "/home/admin1/miniconda3/envs/qiime2-moshpit-2025.10/lib/python3.10/site-packages/q2cli/commands.py", line 639, in _execute_action
results = action(**arguments)
File "", line 2, in fetch_eggnog_db
File "/home/admin1/miniconda3/envs/qiime2-moshpit-2025.10/lib/python3.10/site-packages/qiime2/sdk/action.py", line 265, in bound_callable
outputs = self.callable_executor(
File "/home/admin1/miniconda3/envs/qiime2-moshpit-2025.10/lib/python3.10/site-packages/qiime2/sdk/action.py", line 451, in callable_executor
self.signature.coerce_given_outputs(output_views, output_types,
File "/home/admin1/miniconda3/envs/qiime2-moshpit-2025.10/lib/python3.10/site-packages/qiime2/core/type/signature.py", line 498, in coerce_given_outputs
output = self._create_output_artifact(
File "/home/admin1/miniconda3/envs/qiime2-moshpit-2025.10/lib/python3.10/site-packages/qiime2/core/type/signature.py", line 520, in _create_output_artifact
artifact = qiime2.sdk.Artifact._from_view(
File "/home/admin1/miniconda3/envs/qiime2-moshpit-2025.10/lib/python3.10/site-packages/qiime2/sdk/result.py", line 700, in _from_view
result = transformation(view, validate_level)
File "/home/admin1/miniconda3/envs/qiime2-moshpit-2025.10/lib/python3.10/site-packages/qiime2/core/transform.py", line 68, in transformation
self.validate(view, level=validate_level)
File "/home/admin1/miniconda3/envs/qiime2-moshpit-2025.10/lib/python3.10/site-packages/qiime2/core/transform.py", line 143, in validate
view.validate(level)
File "/home/admin1/miniconda3/envs/qiime2-moshpit-2025.10/lib/python3.10/site-packages/qiime2/plugin/model/directory_format.py", line 183, in validate
raise ValidationError("Unrecognized file (%s) for %s."
qiime2.core.exceptions.ValidationError: Unrecognized file (/tmp/qiime2/admin1/processes/60908-1762251494.91@admin1/tmp/q2-OutPath-qfrjs41x/eggnog.taxa.tar.gz) for EggnogRefDirFmt.

Plugin error from annotate:

Unrecognized file (/tmp/qiime2/admin1/processes/60908-1762251494.91@admin1/tmp/q2-OutPath-qfrjs41x/eggnog.taxa.tar.gz) for EggnogRefDirFmt.

See above for debug info.

The fetch-diamond-db action and fetch-eggnog-db action are using the same database URL (http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog_proteins.dmnd.gz). However, the version 2025.10 only fixed the URL of the fetch-diamond-db action but not update that of the fetch-eggnog-db action. I hope this bug wonā€™t be fixed until the next version.

17

Thanks for sharing your error message, @yawei. I can confirm that the URL that it tries to download is not specified on our end but in this script: eggnog-mapper/download_eggnog_data.py at master Ā· eggnogdb/eggnog-mapper Ā· GitHub. The issue is in EggNOG and is described here. There exists a pull request that updates the broken URL, but it has yet to be integrated into the main branch. We simply wait for EggNOG to fix the URL on their side, and in the meantime I suggest manually downloading the database and then importing it as an artifact.

2 Likes
18

Iā€™ve opened an issue in q2-annotate, referencing this forum post. Iā€™ve also included a step-by-step tutorial on how to manually download and import the EggNOG database as a temporary workaround. I hope that this is helpful to you or anyone else.

4 Likes
19

Hiļ¼Œ@feliciaļ¼Œthank you for your reply and kind effort very much, this help me a lotļ¼

Here is another issue. According to the debug information, this database needs to download two files, eggnog.taxa.db and eggnog.taxa.db. However, the method you provided only downloaded and imported the eggnog.taxa.db file. Is that okay?

Sincerely~

20

Thanks for the feedback, @yawei. Youā€™re right that there is one file missing. In fact, there are actually three files that goes into the directory that you import: eggnog.db, eggnog.taxa.db, eggnog.taxa.db.traverse.pkl. They are all downloadable from the same link (eggnog.taxa.db and eggnog.taxa.db.traverse.pkl are both contained within eggnog.taxa.tar.gz).

Iā€™ve updated the guide to reflect this, hopefully now everything should work without an issue.

3 Likes