can't download HMMs

[185971]

Downloading HMMER database of tax ID taxid as "4751" to /home/xly/mambaforge/envs/fun/lib/python3.8/site-packages/data/hmmer/4751 Note that this can take a long time for large taxonomic levels cd /home/xly/mambaforge/envs/fun/lib/python3.8/site-packages/data/hmmer/4751; echo Downloading HMMs... && wget -nH --user-agent=Mozilla/5.0 --relative -r --no-parent --reject "index.html" --cut-dirs=4 -e robots=off http://eggnog5.embl.de/download/eggnog_5.0/per_tax_level/taxid//taxid_hmms.tar.gz && echo Decompressing HMMs... && tar zxf taxid_hmms.tar.gz && echo taxid/ | xargs mv -t ./ && rm -r taxid && rm taxid_hmms.tar.gz; numf=$(find ./ | grep -c ".hmm$"); curr=0; cat /dev/null > 4751.hmm_tmp; for file in $(find ./ | grep ".hmm$"); do curr=$((curr+1)); echo "merging HMMs... ${file} (${curr}/${numf})"; cat "${file}" | sed -e "s/.faa.final_tree.fa//" -e "s/.faa.final_tree//" >> 4751.hmm_tmp; rm "${file}"; done; mv 4751.hmm_tmp 4751.hmm; (if [ -f 4751.hmm.h3i ]; then rm 4751.hmm.h3; fi) && echo "hmmpress-ing HMMs... " && /home/xly/mambaforge/envs/fun/bin/hmmpress 4751.hmm && echo "generating idmap file... " && cat 4751.hmm | grep "^NAME" | sed -e "s/^NAME //" | awk '{print NR" "$0}' > 4751.hmm.idmap && echo "removing single OG hmm files... " && echo ./*hmm | xargs rm; Downloading HMMs... --2023-07-26 12:57:38-- http://eggnog5.embl.de/download/eggnog_5.0/per_tax_level/taxid//taxid_hmms.tar.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... 404 Not Found 2023-07-26 12:57:39 ERROR 404: Not Found.

merging HMMs... ./4751.hmm (1/1) hmmpress-ing HMMs...

Error: File format problem in trying to open HMM file 4751.hmm. File exists, but appears to be empty?

cd /home/xly/mambaforge/envs/fun/lib/python3.8/site-packages/data/hmmer/4751; echo Downloading FASTAs... && wget -nH --user-agent=Mozilla/5.0 --relative -r --no-parent --reject "index.html" --cut-dirs=4 -e robots=off http://eggnog5.embl.de/download/eggnog_5.0/per_tax_level/taxid//taxid_raw_algs.tar && echo Decompressing FASTAs... && tar xf taxid_raw_algs.tar && echo taxid/ | xargs mv -t ./ && rm -r taxid && rm taxid_raw_algs.tar; numf=$(find ./ | grep -c ".faa.gz$"); curr=0; for file in $(find ./ | grep ".faa.gz$"); do curr=$((curr+1)); echo "processing FASTAs... ${file} (${curr}/${numf})"; outf=$(echo "$file" | sed "s/.raw_alg.faa.gz/.fa/"); zcat "$file" | awk '/^>/{print; next}{gsub("-", ""); print}' > "$outf" && rm "$file"; done Downloading FASTAs... --2023-07-26 12:57:39-- http://eggnog5.embl.de/download/eggnog_5.0/per_tax_level/taxid//taxid_raw_algs.tar 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... 404 Not Found 2023-07-26 12:57:40 ERROR 404: Not Found.

[185971]

Download HMMER database of tax ID taxid? [y,n] y Please, specify a non-empty name for the database (e.g. Bacteria) [default:taxid]: 4751

[Cantalapiedra]

Hi @185971 ,

What command are you using to call the script?

Best, Carlos

[Chrizzy23]

Hello! I have the same problem when trying to download HMMER database with download_eggnog_data.py Did you find a solution @185971 ?

[miferg]

Hi, I have the same problem when running: download_eggnog_data.py -H I am using the conda installation.

[Cantalapiedra]

Dear all,

Please, provide your whole commands which caused the errors, so that I can try to diagnose what is happening. For instance, in the first post, the error is "Downloading HMMER database of tax ID taxid as "4751" to /home/xly/mambaforge/envs/fun/lib/python3.8/site-packages/data/hmmer/4751"

It seems that the script is understanding that you want download taxid = "taxid". Without knowing the exact command that it was used I cannot know if the problems is with how the command was written, or if there is any other problem in the script making the variable take the "taxid" value.

Thank you for your understanding.

Best, Carlos