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Fix: Update obsolete URLs for database download

Open RoshTzsche opened this issue 2 months ago • 4 comments

I found an error with the URLs in "download_eggnog_data.py" script, and fixed it.

You can also use wget to download the databases from the source directly:

wget http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog.db.gz
wget http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog.taxa.tar.gz
wget http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog_proteins.dmnd.gz

You would need to decompress them.

gunzip eggnog.db.gz
tar -xzvf eggnog.taxa.tar.gz
gunzip eggnog_proteins.dmnd.gz

However doing this is more tedious than just running the script.

RoshTzsche avatar Oct 12 '25 18:10 RoshTzsche

Same code as #574

AggressiveHayBale avatar Oct 13 '25 11:10 AggressiveHayBale

Not fixed yet. The error still make it tedious to download manually the data: HTTP request sent, awaiting response... 404 Not Found Replacing the base URL in the download_eggnog_data.py script with https://eggnogdb.org/downloads/ will likely work, or downloading the files manually will have the same effect. I'm not sure if the filenames matter (they've changed too). We would be very happy if the download_eggnog_data.py script were updated with the correct URL.

41ison avatar Nov 15 '25 19:11 41ison

(eggnog) mahe@pop-os:~$ wget http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog.db.gz wget http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog.taxa.tar.gz wget http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog_proteins.dmnd.gz --2025-12-08 13:14:05-- 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 9.65MB/s in 1m 44s

2025-12-08 13:15:50 (9.96 MB/s) - Connection closed at byte 1086930798. Retrying.

--2025-12-08 13:15:51-- (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), 5690046325 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-08 13:15:52 (182 MB/s) - Read error at byte 1086937699/6776977123 (Connection reset by peer). Retrying.

--2025-12-08 13:15:54-- (try: 3) 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), 5690039424 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’ even it failing i tried v6 URL and manually also exactly it is filing after 1.01 gb

thom-ST avatar Dec 08 '25 07:12 thom-ST

wget http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog.db.gz wget http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog.taxa.tar.gz wget http://eggnog5.embl.de/download/emapperdb-5.0.2/eggnog_proteins.dmnd.gz (eggnog) mahe@pop-os:~/SURE-Pipe$ download_eggnog_data.py Download main annotation database? [y,n] y Downloading "eggnog.db" at /home/mahe/miniconda3/envs/eggnog/lib/python3.10/site-packages/data... cd /home/mahe/miniconda3/envs/eggnog/lib/python3.10/site-packages/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://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz && echo Decompressing... && gunzip eggnog.db.gz --2025-12-11 16:17:27-- http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Resolving eggnog6.embl.de (eggnog6.embl.de)... 194.94.44.170 Connecting to eggnog6.embl.de (eggnog6.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 10.5MB/s in 1m 44s

2025-12-11 16:19:11 (9.93 MB/s) - Connection closed at byte 1086911798. Retrying.

--2025-12-11 16:19:12-- (try: 2) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5690065325 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:19:13 (175 MB/s) - Read error at byte 1086918699/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:19:15-- (try: 3) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5690058424 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:19:15 (311 MB/s) - Read error at byte 1086925600/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:19:18-- (try: 4) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5690051523 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:19:19 (272 MB/s) - Read error at byte 1086932501/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:19:23-- (try: 5) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5690044622 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:19:23 (229 MB/s) - Read error at byte 1086937954/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:19:28-- (try: 6) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5690039169 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:19:28 (281 MB/s) - Read error at byte 1086944855/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:19:34-- (try: 7) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5690032268 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:19:35 (281 MB/s) - Read error at byte 1086951756/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:19:42-- (try: 8) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5690025367 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:19:42 (271 MB/s) - Read error at byte 1086958657/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:19:50-- (try: 9) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5690018466 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:19:51 (240 MB/s) - Read error at byte 1086964110/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:20:00-- (try:10) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5690013013 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:20:00 (36.8 MB/s) - Read error at byte 1086971011/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:20:10-- (try:11) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5690006112 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:20:10 (369 MB/s) - Read error at byte 1086977912/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:20:20-- (try:12) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5689999211 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:20:21 (742 MB/s) - Read error at byte 1086983365/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:20:31-- (try:13) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5689993758 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:20:31 (212 MB/s) - Read error at byte 1086988818/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:20:41-- (try:14) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5689988305 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:20:42 (245 MB/s) - Read error at byte 1086994271/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:20:52-- (try:15) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5689982852 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:20:52 (278 MB/s) - Read error at byte 1087001172/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:21:02-- (try:16) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5689975951 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:21:02 (308 MB/s) - Read error at byte 1087008073/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:21:12-- (try:17) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5689969050 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:21:13 (234 MB/s) - Read error at byte 1087013526/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:21:23-- (try:18) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5689963597 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:21:23 (1.17 GB/s) - Read error at byte 1087020427/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:21:33-- (try:19) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5689956696 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:21:34 (989 MB/s) - Read error at byte 1087027328/6776977123 (Connection reset by peer). Retrying.

--2025-12-11 16:21:44-- (try:20) http://eggnog6.embl.de/download/emapperdb-5.0.2/eggnog.db.gz Connecting to eggnog6.embl.de (eggnog6.embl.de)|194.94.44.170|:80... connected. HTTP request sent, awaiting response... 206 Partial Content Length: 6776977123 (6.3G), 5689949795 (5.3G) remaining [application/octet-stream] Saving to: ‘eggnog.db.gz’

eggnog.db.gz 16%[++++++++++++++++ ] 1.01G --.-KB/s in 0s

2025-12-11 16:21:44 (278 MB/s) - Read error at byte 1087034229/6776977123 (Connection reset by peer). Giving up.

BPaul-bioinfoLAB avatar Dec 15 '25 03:12 BPaul-bioinfoLAB