soedinglab
Error in expand aln
Core dumped and crashed when running expand aln command using the recent mmseqs version.
The following is what I ran: `#!/bin/bash -e MMSEQS="mmseqs" QUERY=<query_path> BASE=<output_path> DB1="database/mmseqs/uniref30/uniref30_2302_db" DB2="" DB3="" USE_ENV="0" USE_TEMPLATES="0" FILTER="1" TAXONOMY="0" M8OUT="0" EXPAND_EVAL=inf ALIGN_EVAL=10 DIFF=3000 QSC=-20.0 MAX_ACCEPT=1000000 if [ "${FILTER}" = "1" ]; then 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 --k-score 'seq:96,prof:80' -e 0.1 --max-seqs 10000" FILTER_PARAM="--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}" "${BASE}/qdb" --dbtype 1 "${MMSEQS}" search "${BASE}/qdb" "${DB1}" "${BASE}/res" "${BASE}/tmp1" $SEARCH_PARAM "${MMSEQS}" mvdb "${BASE}/tmp1/latest/profile_1" "${BASE}/prof_res" "${MMSEQS}" lndb "${BASE}/qdb_h" "${BASE}/prof_res_h"
(
"${MMSEQS}" expandaln "${BASE}/qdb" "${DB1}.idx" "${BASE}/res" "${DB1}.idx" "${BASE}/res_exp" --db-load-mode 2 ${EXPAND_PARAM} "${MMSEQS}" align "${BASE}/prof_res" "${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 "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_exp_realign" "${BASE}/res_exp_realign_filter" --db-load-mode 2 --qid 0 --qsc $QSC --diff 0 --max-seq-id 1.0 --filter-min-enable 100 if [ "${M8OUT}" = "1" ]; then "${MMSEQS}" filterresult "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_exp_realign_filter" "${BASE}/res_exp_realign_filter_filter" --db-load-mode 2 ${FILTER_PARAM} "${MMSEQS}" convertalis "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_exp_realign_filter_filter" "${BASE}/uniref.m8" --db-load-mode 2 --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,tseq "${MMSEQS}" rmdb "${BASE}/res_exp_realign_filter_filter" else "${MMSEQS}" result2msa "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_exp_realign_filter" "${BASE}/uniref.a3m" --msa-format-mode 6 --db-load-mode 2 --filter-msa ${FILTER} ${FILTER_PARAM} fi "${MMSEQS}" rmdb "${BASE}/res_exp_realign" "${MMSEQS}" rmdb "${BASE}/res_exp" "${MMSEQS}" rmdb "${BASE}/res" if [ "${TAXONOMY}" = "1" ] && [ -e "${DB1}_taxonomy" ]; then "${MMSEQS}" convertalis "${BASE}/qdb" "${DB1}.idx" "${BASE}/res_exp_realign_filter" "${BASE}/res_exp_realign_tax" --db-output 1 --format-output "taxid,target,taxlineage" --db-load-mode 2 awk 'BEGIN { printf("%c%c%c%c",8,0,0,0); exit; }' > "${BASE}/res_exp_realign_tax.dbtype" MMSEQS_FORCE_MERGE=1 "${MMSEQS}" filtertaxdb "${DB1}" "${BASE}/res_exp_realign_tax" "${BASE}/res_exp_realign_tax_filt" --taxon-list '!12908&&!28384' tr -d '\000' < "${BASE}/res_exp_realign_tax_filt" | sort -u > "${BASE}/uniref_tax.tsv" fi "${MMSEQS}" rmdb "${BASE}/res_exp_realign_filter"
)& (
if [ "${USE_TEMPLATES}" = "1" ]; then "${MMSEQS}" search "${BASE}/prof_res" "${DB2}" "${BASE}/res_pdb" "${BASE}/tmp2" --db-load-mode 2 -s 7.5 -a -e 0.1 "${MMSEQS}" convertalis "${BASE}/prof_res" "${DB2}.idx" "${BASE}/res_pdb" "${BASE}/pdb70.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 "${BASE}/prof_res" "${DB3}" "${BASE}/res_env" "${BASE}/tmp3" $SEARCH_PARAM "${MMSEQS}" expandaln "${BASE}/prof_res" "${DB3}.idx" "${BASE}/res_env" "${DB3}.idx" "${BASE}/res_env_exp" -e ${EXPAND_EVAL} --expansion-mode 0 --db-load-mode 2 "${MMSEQS}" align "${BASE}/tmp3/latest/profile_1" "${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 "${BASE}/qdb" "${DB3}.idx" "${BASE}/res_env_exp_realign" "${BASE}/res_env_exp_realign_filter" --db-load-mode 2 --qid 0 --qsc $QSC --diff 0 --max-seq-id 1.0 --filter-min-enable 100 if [ "${M8OUT}" = "1" ]; then "${MMSEQS}" filterresult "${BASE}/qdb" "${DB3}.idx" "${BASE}/res_env_exp_realign_filter" "${BASE}/res_env_exp_realign_filter_filter" --db-load-mode 2 ${FILTER_PARAM} "${MMSEQS}" convertalis "${BASE}/qdb" "${DB3}.idx" "${BASE}/res_env_exp_realign_filter_filter" "${BASE}/bfd.mgnify30.metaeuk30.smag30.m8" --db-load-mode 2 --format-output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,tseq "${MMSEQS}" rmdb "${BASE}/res_env_exp_realign_filter_filter" else "${MMSEQS}" result2msa "${BASE}/qdb" "${DB3}.idx" "${BASE}/res_env_exp_realign_filter" "${BASE}/bfd.mgnify30.metaeuk30.smag30.a3m" --msa-format-mode 6 --db-load-mode 2 --filter-msa ${FILTER} ${FILTER_PARAM} fi "${MMSEQS}" rmdb "${BASE}/res_env_exp_realign_filter" "${MMSEQS}" rmdb "${BASE}/res_env_exp_realign" "${MMSEQS}" rmdb "${BASE}/res_env_exp" "${MMSEQS}" rmdb "${BASE}/res_env" fi
)& wait
"${MMSEQS}" rmdb "${BASE}/qdb" "${MMSEQS}" rmdb "${BASE}/qdb_h" "${MMSEQS}" rmdb "${BASE}/res" rm -f -- "${BASE}/prof_res"* rm -rf -- "${BASE}/tmp1" "${BASE}/tmp2" "${BASE}/tmp3"`
#The following is the error I get Index version: 16 Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42 ScoreMatrix: VTML80.out Index version: 16 Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42 ScoreMatrix: VTML80.out [> ] 0.00% 1 eta [================> ] 25.00% 2 eta[================================> ] 50.00% 3 eta[================================================> ] 75.00% 4 etafree(): invalid next size (normal) ./msa.sh: line 58: 98650 Aborted (core dumped) "${MMSEQS}" expandaln "${BASE}/qdb" "${DB1}.idx" "${BASE}/res" "${DB1}.idx" "${BASE}/res_exp" --db-load-mode 2 ${EXPAND_PARAM}
