Created
September 27, 2021 17:46
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ColabFoldMMseqs2Script
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#!/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}/${DB2}.m8" --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,cigar --db-load-mode 2 | |
"${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}" 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" |
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