MMseqs2 search results with Taxonomy ID using uniref30_2103 database and colabfold_envdb_202108 database

[Starmie21]

Dear friends, we got some trouble for MSA searching contain Taxonomy ID annotation.

Expected Behavior

We want to search using mmseqs2 with uniref30_2103 database and colabfold_envdb_202108 database. We want the results with the Taxonomy ID annotation for each sequence in MSA.

Current Behavior

We used a modified version of colabfold_search.sh, only with a modification from the convertail commend for Taxonomy ID as follows:

"${MMSEQS}" convertalis "${BASE}/prof_res" "${DBBASE}/${DB2}.idx" "${BASE}/res_pdb" "${BASE}/${DB2}.m8" --format-output query,target,taxid,taxname,taxlineage,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,cigar --db-load-mode 2

After search, we found the "taxid,taxname,taxlineage" not in the MSA results. Is that because the pre-compiled dbs(uniref30_2103 database and colabfold_envdb_202108 database) does not contain the Taxonomy ID annotation? We also found the uniref30_2103_taxonomy.tar.gz updated on the website, please help us on how to make use of it, thank you~

[Starmie21]

This is the full script we used now

!/bin/bash -e

MMSEQS="$1" QUERY="$2" DBBASE="$3" BASE="$4" DB1="$5" DB2="$6" DB3="$7" USE_ENV="$8" USE_TEMPLATES="$9" FILTER="${10}" EXPAND_EVAL=inf ALIGN_EVAL=10 DIFF=3000 QSC=-20.0 MAX_ACCEPT=1000000 if [ "${FILTER}" = "1" ]; then

0.1 was not used in benchmarks due to POSIX shell bug in line above

EXPAND_EVAL=0.1

ALIGN_EVAL=10 QSC=0.8 MAX_ACCEPT=100000 fi export MMSEQS_CALL_DEPTH=1 SEARCH_PARAM="--num-iterations 3 --db-load-mode 2 -a -s 8 -e 0.1 --max-seqs 10000" FILTER_PARAM="--filter-msa ${FILTER} --filter-min-enable 1000 --diff ${DIFF} --qid 0.0,0.2,0.4,0.6,0.8,1.0 --qsc 0 --max-seq-id 0.95" EXPAND_PARAM="--expansion-mode 0 -e ${EXPAND_EVAL} --expand-filter-clusters ${FILTER} --max-seq-id 0.95" mkdir -p "${BASE}" "${MMSEQS}" createdb "${QUERY}" "${BASE}/qdb" "${MMSEQS}" search "${BASE}/qdb" "${DBBASE}/${DB1}" "${BASE}/res" "${BASE}/tmp" $SEARCH_PARAM "${MMSEQS}" expandaln "${BASE}/qdb" "${DBBASE}/${DB1}.idx" "${BASE}/res" "${DBBASE}/${DB1}.idx" "${BASE}/res_exp" --db-load-mode 2 ${EXPAND_PARAM} "${MMSEQS}" mvdb "${BASE}/tmp/latest/profile_1" "${BASE}/prof_res" "${MMSEQS}" lndb "${BASE}/qdb_h" "${BASE}/prof_res_h" "${MMSEQS}" align "${BASE}/prof_res" "${DBBASE}/${DB1}.idx" "${BASE}/res_exp" "${BASE}/res_exp_realign" --db-load-mode 2 -e ${ALIGN_EVAL} --max-accept ${MAX_ACCEPT} --alt-ali 10 -a "${MMSEQS}" filterresult "${BASE}/qdb" "${DBBASE}/${DB1}.idx" "${BASE}/res_exp_realign" "${BASE}/res_exp_realign_filter" --db-load-mode 2 --qid 0 --qsc $QSC --diff 0 --max-seq-id 1.0 --filter-min-enable 100 "${MMSEQS}" result2msa "${BASE}/qdb" "${DBBASE}/${DB1}.idx" "${BASE}/res_exp_realign_filter" "${BASE}/uniref.a3m" --msa-format-mode 6 --db-load-mode 2 ${FILTER_PARAM} "${MMSEQS}" rmdb "${BASE}/res_exp_realign" "${MMSEQS}" rmdb "${BASE}/res_exp" "${MMSEQS}" rmdb "${BASE}/res" "${MMSEQS}" rmdb "${BASE}/res_exp_realign_filter" if [ "${USE_TEMPLATES}" = "1" ]; then "${MMSEQS}" search "${BASE}/prof_res" "${DBBASE}/${DB2}" "${BASE}/res_pdb" "${BASE}/tmp" --db-load-mode 2 -s 7.5 -a -e 0.1 "${MMSEQS}" convertalis "${BASE}/prof_res" "${DBBASE}/${DB2}.idx" "${BASE}/res_pdb" "${BASE}/${DB2}.m8" --format-output query,target,taxid,taxname,taxlineage,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,cigar --db-load-mode 2 "${MMSEQS}" rmdb "${BASE}/res_pdb" fi if [ "${USE_ENV}" = "1" ]; then "${MMSEQS}" search "${BASE}/prof_res" "${DBBASE}/${DB3}" "${BASE}/res_env" "${BASE}/tmp" $SEARCH_PARAM "${MMSEQS}" expandaln "${BASE}/prof_res" "${DBBASE}/${DB3}.idx" "${BASE}/res_env" "${DBBASE}/${DB3}.idx" "${BASE}/res_env_exp" -e ${EXPAND_EVAL} --expansion-mode 0 --db-load-mode 2 "${MMSEQS}" convertalis "${BASE}/prof_res" "${DBBASE}/${DB2}.idx" "${BASE}/res_pdb" "${BASE}/${DB2}.m8" --format-output query,target,taxid,taxname,taxlineage,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,cigar --db-load-mode 2 "${MMSEQS}" align "${BASE}/tmp/latest/profile_1" "${DBBASE}/${DB3}.idx" "${BASE}/res_env_exp" "${BASE}/res_env_exp_realign" --db-load-mode 2 -e ${ALIGN_EVAL} --max-accept ${MAX_ACCEPT} --alt-ali 10 -a "${MMSEQS}" filterresult "${BASE}/qdb" "${DBBASE}/${DB3}.idx" "${BASE}/res_env_exp_realign" "${BASE}/res_env_exp_realign_filter" --db-load-mode 2 --qid 0 --qsc $QSC --diff 0 --max-seq-id 1.0 --filter-min-enable 100 "${MMSEQS}" result2msa "${BASE}/qdb" "${DBBASE}/${DB3}.idx" "${BASE}/res_env_exp_realign_filter" "${BASE}/bfd.mgnify30.metaeuk30.smag30.a3m" --msa-format-mode 6 --db-load-mode 2 ${FILTER_PARAM} "${MMSEQS}" rmdb "${BASE}/res_env_exp_realign_filter" "${MMSEQS}" rmdb "${BASE}/res_env_exp_realign" "${MMSEQS}" rmdb "${BASE}/res_env_exp" "${MMSEQS}" rmdb "${BASE}/res_env" fi "${MMSEQS}" rmdb "${BASE}/qdb" "${MMSEQS}" rmdb "${BASE}/qdb_h" "${MMSEQS}" rmdb "${BASE}/res" rm -f -- "${BASE}/prof_res"* rm -rf -- "${BASE}/tmp"

[martin-steinegger]

ColabfoldDB does not contain taxonomical information since the sequences are from various metagenomic sources, only UniRef30 has taxonomical information. We recently uploaded the UniRef taxonomy information to our ftp colabfold.mmseqs.com. You can just download the taxonomy file and unzip it in the fold where the database is located. The following command should give you a TSV file containing the tax info for the UniRef:

"${MMSEQS}" convertalis "${BASE}/qdb" "${DBBASE}/${DB1}.idx" "${BASE}/res_exp_realign_filter" "${BASE}/uniref_tax.m8" --format-output query,target,taxid,taxname,taxlineage,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,cigar --db-load-mode 2

[Starmie21]

Thank you very much ~~

[AidanAbd]

Hello, ran into the same issue above with the upgraded uniref -- is the uniref30_2202 taxonomy available on your ftp site or could you explain how I can generate it myself? Thank you.