download_eggnog_data.py not working: ERROR 404: Not Found.

[g0ddengr]

Have the urls to eggNOG v5 db files changed? The download script isn't working.

$ download_eggnog_data.py -P -M --data_dir /data/re
ference/eggnog-mapper/2.1.13
Download main annotation database? [y,n] y
Downloading "eggnog.db" at /data/reference/eggnog-mapper/2.1.13...
cd /data/reference/eggnog-mapper/2.1.13 && 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
--2025-12-05 09:59:05-- 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
2025-12-05 09:59:05 ERROR 404: Not Found.

Download taxa database? [y,n] y
Downloading "eggnog.taxa.db" at /data/reference/eggnog-mapper/2.1.13...
cd /data/reference/eggnog-mapper/2.1.13 && 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
--2025-12-05 09:59:07-- 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
2025-12-05 09:59:07 ERROR 404: Not Found.

Download diamond database (~4GB after decompression)? [y,n] y
Downloading fasta files " at /data/reference/eggnog-mapper/2.1.13...
cd /data/reference/eggnog-mapper/2.1.13 && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O eggnog_proteins.dmnd.gz http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog_proteins.dmnd.gz && echo Decompressing... && gunzip eggnog_proteins.dmnd.gz
--2025-12-05 09:59:08-- http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog_proteins.dmnd.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
2025-12-05 09:59:08 ERROR 404: Not Found.

Skipping novel families diamond and annotation databases (or already present). Use -F and -f to force download
Download pfam database (~3GB after decompression)? [y,n] y
Downloading Pfam files " at /data/reference/eggnog-mapper/2.1.13...
cd /data/reference/eggnog-mapper/2.1.13 && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O pfam.tar.gz http://eggnogdb.embl.de/download/emapperdb-5.0.2/pfam.tar.gz && echo Decompressing... && tar -zxf pfam.tar.gz && rm pfam.tar.gz
--2025-12-05 09:59:10-- http://eggnogdb.embl.de/download/emapperdb-5.0.2/pfam.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
2025-12-05 09:59:10 ERROR 404: Not Found.

Download MMseqs2 database (~10GB after decompression)? [y,n] y
Downloading MMseqs2 files " at /data/reference/eggnog-mapper/2.1.13...
cd /data/reference/eggnog-mapper/2.1.13 && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O mmseqs.tar.gz http://eggnogdb.embl.de/download/emapperdb-5.0.2/mmseqs.tar.gz && echo Decompressing... && tar -zxf mmseqs.tar.gz && rm mmseqs.tar.gz
--2025-12-05 09:59:11-- http://eggnogdb.embl.de/download/emapperdb-5.0.2/mmseqs.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
2025-12-05 09:59:11 ERROR 404: Not Found.

No HMMER database requested. Use "-H -d taxid" to download the hmmer database for taxid
Finished.

[thom-ST]

(eggnog) mahe@pop-os:~$ download_eggnog_data.py -y --data_dir ~/eggnog_data -D -F -M
Downloading "eggnog.db" at /home/mahe/eggnog_data...
cd /home/mahe/eggnog_data && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O eggnog.db.gz http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog.db.gz && echo Decompressing... && gunzip eggnog.db.gz
--2025-12-06 12:47:51-- http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog.db.gz
Resolving eggnog5.embl.de (eggnog5.embl.de)... 194.94.44.170
Connecting to eggnog5.embl.de (eggnog5.embl.de)|194.94.44.170|:80... connected.
HTTP request sent, awaiting response... 200 OK
Length: 6776977123 (6.3G) [application/octet-stream]
Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[===============> ] 1.01G 10.7MB/s in 93s

2025-12-06 12:49:24 (11.2 MB/s) - Connection closed at byte 1086935382. Retrying.

--2025-12-06 12:49:25-- (try: 2) http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog.db.gz
Connecting to eggnog5.embl.de (eggnog5.embl.de)|194.94.44.170|:80... connected.
HTTP request sent, awaiting response... 206 Partial Content
Length: 6776977123 (6.3G), 5690041741 (5.3G) remaining [application/octet-stream]
Saving to: ‘eggnog.db.gz’
am getting this error while running its not downloading full why

[eggrandio]

It seems that the URL for the databases has changed from eggnogdb to eggnog5. You can modify the script manually:

sed -i 's|eggnogdb.embl.de|eggnog5.embl.de|g' ~/miniconda3/bin/download_eggnog_data.py
download_eggnog_data.py

[thom-ST]

I tried eggnog5...also and eggnog6 also...but some databases it's not downloading beyond 1.01 gb in manually also intried same நன்றி மற்றும் வணக்கங்கள் இன்பன்ட் தாமஸ்.சூ

…

On Tue, 9 Dec, 2025, 7:44 pm Eduardo Gonzalez Grandio, < ***@***.***> wrote: *eggrandio* left a comment (eggnogdb/eggnog-mapper#587) <#587 (comment)> It seems that the URL for the databases has changed from eggnogdb to eggnog5. You can modify the script manually: sed -i 's|eggnogdb.embl.de|eggnog5.embl.de|g' ~/miniconda3/bin/download_eggnog_data.py download_eggnog_data.py — Reply to this email directly, view it on GitHub <#587 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BF56DNI53AE4IYO56XQHIW34A3KNLAVCNFSM6AAAAACOFGHO62VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTMMZSGQ4DAOJSGQ> . You are receiving this because you commented.Message ID: ***@***.***>

[Felipe-ia]

Hi, I'm having the same problem. Any solutions?

=====================================================================================================
(/media/mordor/fcasais/EggNOGmapper_testing/Eggnog_teste) fcasais@arya:/media/mordor/fcasais/EggNOGmapper_testing$ download_eggnog_data.py -F -P -M --data_dir Database_egg/
Download main annotation database? [y,n] y
Downloading "eggnog.db" at /media/mordor/fcasais/EggNOGmapper_testing/Database_egg...
cd /media/mordor/fcasais/EggNOGmapper_testing/Database_egg && 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
--2025-12-10 13:30:24-- 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
2025-12-10 13:30:25 ERROR 404: Not Found.

Download taxa database? [y,n] y
Downloading "eggnog.taxa.db" at /media/mordor/fcasais/EggNOGmapper_testing/Database_egg...
cd /media/mordor/fcasais/EggNOGmapper_testing/Database_egg && 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
--2025-12-10 13:30:29-- 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
2025-12-10 13:30:30 ERROR 404: Not Found.

Download diamond database (~4GB after decompression)? [y,n] y
Downloading fasta files " at /media/mordor/fcasais/EggNOGmapper_testing/Database_egg...
cd /media/mordor/fcasais/EggNOGmapper_testing/Database_egg && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O eggnog_proteins.dmnd.gz http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog_proteins.dmnd.gz && echo Decompressing... && gunzip eggnog_proteins.dmnd.gz
--2025-12-10 13:30:31-- http://eggnogdb.embl.de/download/emapperdb-5.0.2/eggnog_proteins.dmnd.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
2025-12-10 13:30:32 ERROR 404: Not Found.

Download novel families diamond and annotation databases (1.3GB after decompression)? [y,n] y
Downloading novel families files " at /media/mordor/fcasais/EggNOGmapper_testing/Database_egg...
cd /media/mordor/fcasais/EggNOGmapper_testing/Database_egg && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O novel_fams.dmnd.gz http://eggnogdb.embl.de/download/novel_fams-1.0.1/novel_fams.dmnd.gz && echo Decompressing... && gunzip novel_fams.dmnd.gz
--2025-12-10 13:30:59-- http://eggnogdb.embl.de/download/novel_fams-1.0.1/novel_fams.dmnd.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
2025-12-10 13:30:59 ERROR 404: Not Found.

cd /media/mordor/fcasais/EggNOGmapper_testing/Database_egg && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O novel_fams.pkl.gz http://eggnogdb.embl.de/download/novel_fams-1.0.1/novel_fams.pkl.gz && echo Decompressing... && gunzip novel_fams.pkl.gz
--2025-12-10 13:30:59-- http://eggnogdb.embl.de/download/novel_fams-1.0.1/novel_fams.pkl.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
2025-12-10 13:31:00 ERROR 404: Not Found.

Download pfam database (~3GB after decompression)? [y,n] y
Downloading Pfam files " at /media/mordor/fcasais/EggNOGmapper_testing/Database_egg...
cd /media/mordor/fcasais/EggNOGmapper_testing/Database_egg && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O pfam.tar.gz http://eggnogdb.embl.de/download/emapperdb-5.0.2/pfam.tar.gz && echo Decompressing... && tar -zxf pfam.tar.gz && rm pfam.tar.gz
--2025-12-10 13:31:01-- http://eggnogdb.embl.de/download/emapperdb-5.0.2/pfam.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
2025-12-10 13:31:02 ERROR 404: Not Found.

Download MMseqs2 database (~10GB after decompression)? [y,n] y
Downloading MMseqs2 files " at /media/mordor/fcasais/EggNOGmapper_testing/Database_egg...
cd /media/mordor/fcasais/EggNOGmapper_testing/Database_egg && wget -nH --user-agent=Mozilla/5.0 --relative --no-parent --reject "index.html*" --cut-dirs=4 -e robots=off -O mmseqs.tar.gz http://eggnogdb.embl.de/download/emapperdb-5.0.2/mmseqs.tar.gz && echo Decompressing... && tar -zxf mmseqs.tar.gz && rm mmseqs.tar.gz
--2025-12-10 13:31:02-- http://eggnogdb.embl.de/download/emapperdb-5.0.2/mmseqs.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
2025-12-10 13:31:03 ERROR 404: Not Found.

No HMMER database requested. Use "-H -d taxid" to download the hmmer database for taxid
Finished.

[AggressiveHayBale]

@Felipe-ia
Please look at #574 pull request and issue #571 to understand the issue. Basically they changed the download address but havent updated the downloading script. The fix is a simple change of 2 lines of code

[leichen-oc]

@Felipe-ia Please look at #574 pull request and issue #571 to understand the issue. Basically they changed the download address but havent updated the downloading script. The fix is a simple change of 2 lines of code请查看 #574 拉取请求和问题 #571 ，以了解问题所在。基本上他们改了下载地址，但下载脚本还没更新。解决办法就是简单地修改两行代码

thinks

[anthony-aylward]

For anyone waiting for this to be implemented, for my own convenience I've written a Python package to make the fix in a simple way. See it on PyPI, in case you find it useful:

https://pypi.org/project/eggnog-mapper-fixurl/