MMseqs2
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soedinglab
when I use GPU to accelarate colabfold_search , it slower than colabfold_search by using cpu
One sequence query will take about one hour and --gpu-server 1 doesn't make sense
env：
- 56 vcpu
- 4 X A100 GPU
mmseqs (support gpu): MMseqs2 Version: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
here is my step:
GPU=1 ./setup_databases.sh /ai/sequencedb/colabfold_db
mmseqs gpuserver /ai/sequencedb/colabfold_db/colabfold_envdb_202108_db --max-seqs 10000 --db-load-mode 0 --prefilter-mode 1 &
PID1=$!
mmseqs gpuserver /ai/sequencedb/colabfold_db/uniref30_2302_db --max-seqs 10000 --db-load-mode 0 --prefilter-mode 1 &
PID2=$!
colabfold_search --mmseqs mmseqs --gpu 1 --gpu-server 1 /ai/share/workspace/data/test.fasta /ai/sequencedb/colabfold_db/ ~/result/out5/
log
createdb /root/result/out9/query.fas /root/result/out9/qdb --shuffle 0
Converting sequences
[
Time for merging to qdb_h: 0h 0m 0s 0ms
Time for merging to qdb: 0h 0m 0s 0ms
Database type: Aminoacid
Time for processing: 0h 0m 0s 4ms
Create directory /root/result/out9/tmp
search /root/result/out9/qdb /ai/sequencedb/colabfold_db/uniref30_2302_db /root/result/out9/res /root/result/out9/tmp --threads 64 --num-iterations 3 --db-load-mode 0 -a -e 0.1 --max-seqs 10000 --gpu 1 --prefilter-mode 1
ungappedprefilter /root/result/out9/qdb /ai/sequencedb/colabfold_db/uniref30_2302_db.idx /root/result/out9/tmp/5640223795513751843/pref_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -c 0 -e 0.1 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --min-ungapped-score 15 --max-seqs 10000 --db-load-mode 0 --gpu 1 --gpu-server 0 --gpu-server-wait-timeout 600 --prefilter-mode 1 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
[=================================================================] 1 1s 915ms
Time for merging to pref_0: 0h 0m 0s 0ms
Time for processing: 0h 0m 25s 539ms
align /root/result/out9/qdb /ai/sequencedb/colabfold_db/uniref30_2302_db.idx /root/result/out9/tmp/5640223795513751843/pref_0 /root/result/out9/tmp/5640223795513751843/aln_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 1 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.1 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 1 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Compute score only
Query database size: 1 type: Aminoacid
Target database size: 36293491 type: Aminoacid
Calculation of alignments
[=================================================================] 1 0s 4ms
Time for merging to aln_0: 0h 0m 0s 0ms
10000 alignments calculated
1563 sequence pairs passed the thresholds (0.156300 of overall calculated)
1563.000000 hits per query sequence
Time for processing: 0h 0m 19s 651ms
result2profile /root/result/out9/qdb /ai/sequencedb/colabfold_db/uniref30_2302_db.idx /root/result/out9/tmp/5640223795513751843/aln_0 /root/result/out9/tmp/5640223795513751843/profile_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -e 0.1 --mask-profile 1 --e-profile 0.1 --comp-bias-corr 1 --comp-bias-corr-scale 1 --wg 0 --allow-deletion 0 --filter-msa 1 --filter-min-enable 0 --max-seq-id 0.9 --qid '0.0' --qsc -20 --cov 0 --diff 1000 --pseudo-cnt-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --db-load-mode 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --threads 64 --compressed 0 -v 3 --profile-output-mode 0
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Query database size: 1 type: Aminoacid
Target database size: 36293491 type: Aminoacid
[=================================================================] 1 0s 5ms
Time for merging to profile_0: 0h 0m 0s 0ms
Time for processing: 0h 0m 18s 695ms
ungappedprefilter /root/result/out9/tmp/5640223795513751843/profile_0 /ai/sequencedb/colabfold_db/uniref30_2302_db.idx /root/result/out9/tmp/5640223795513751843/pref_tmp_1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -c 0 -e 0.1 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --min-ungapped-score 15 --max-seqs 10000 --db-load-mode 0 --gpu 1 --gpu-server 0 --gpu-server-wait-timeout 600 --prefilter-mode 1 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
[=================================================================] 1 2s 441ms
Time for merging to pref_tmp_1: 0h 0m 0s 0ms
Time for processing: 0h 0m 21s 13ms
subtractdbs /root/result/out9/tmp/5640223795513751843/pref_tmp_1 /root/result/out9/tmp/5640223795513751843/aln_0 /root/result/out9/tmp/5640223795513751843/pref_1 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3
subtractdbs /root/result/out9/tmp/5640223795513751843/pref_tmp_1 /root/result/out9/tmp/5640223795513751843/aln_0 /root/result/out9/tmp/5640223795513751843/pref_1 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3
Remove /root/result/out9/tmp/5640223795513751843/aln_0 ids from /root/result/out9/tmp/5640223795513751843/pref_tmp_1
[=================================================================] 1 0s 4ms
Time for merging to pref_1: 0h 0m 0s 2ms
Time for processing: 0h 0m 0s 18ms
rmdb /root/result/out9/tmp/5640223795513751843/pref_tmp_1
Time for processing: 0h 0m 0s 1ms
align /root/result/out9/tmp/5640223795513751843/profile_0 /ai/sequencedb/colabfold_db/uniref30_2302_db.idx /root/result/out9/tmp/5640223795513751843/pref_1 /root/result/out9/tmp/5640223795513751843/aln_tmp_1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 1 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.1 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Compute score, coverage and sequence identity
Query database size: 1 type: Profile
Target database size: 36293491 type: Aminoacid
Calculation of alignments
[=================================================================] 1 0s 7ms
Time for merging to aln_tmp_1: 0h 0m 0s 0ms
8448 alignments calculated
1015 sequence pairs passed the thresholds (0.120147 of overall calculated)
1015.000000 hits per query sequence
Time for processing: 0h 0m 18s 683ms
mergedbs /root/result/out9/tmp/5640223795513751843/profile_0 /root/result/out9/tmp/5640223795513751843/aln_1 /root/result/out9/tmp/5640223795513751843/aln_0 /root/result/out9/tmp/5640223795513751843/aln_tmp_1
Merging the results to /root/result/out9/tmp/5640223795513751843/aln_1
[=================================================================] 1 0s 1ms
Time for merging to aln_1: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 4ms
rmdb /root/result/out9/tmp/5640223795513751843/aln_0
Time for processing: 0h 0m 0s 1ms
rmdb /root/result/out9/tmp/5640223795513751843/aln_tmp_1
Time for processing: 0h 0m 0s 1ms
result2profile /root/result/out9/tmp/5640223795513751843/profile_0 /ai/sequencedb/colabfold_db/uniref30_2302_db.idx /root/result/out9/tmp/5640223795513751843/aln_1 /root/result/out9/tmp/5640223795513751843/profile_1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -e 0.1 --mask-profile 1 --e-profile 0.1 --comp-bias-corr 1 --comp-bias-corr-scale 1 --wg 0 --allow-deletion 0 --filter-msa 1 --filter-min-enable 0 --max-seq-id 0.9 --qid '0.0' --qsc -20 --cov 0 --diff 1000 --pseudo-cnt-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --db-load-mode 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --threads 64 --compressed 0 -v 3 --profile-output-mode 0
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Query database size: 1 type: Profile
Target database size: 36293491 type: Aminoacid
[=================================================================] 1 0s 8ms
Time for merging to profile_1: 0h 0m 0s 0ms
Time for processing: 0h 0m 17s 753ms
ungappedprefilter /root/result/out9/tmp/5640223795513751843/profile_1 /ai/sequencedb/colabfold_db/uniref30_2302_db.idx /root/result/out9/tmp/5640223795513751843/pref_tmp_2 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -c 0 -e 0.1 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --min-ungapped-score 15 --max-seqs 10000 --db-load-mode 0 --gpu 1 --gpu-server 0 --gpu-server-wait-timeout 600 --prefilter-mode 1 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
[=================================================================] 1 1s 960ms
Time for merging to pref_tmp_2: 0h 0m 0s 0ms
Time for processing: 0h 0m 20s 324ms
subtractdbs /root/result/out9/tmp/5640223795513751843/pref_tmp_2 /root/result/out9/tmp/5640223795513751843/aln_1 /root/result/out9/tmp/5640223795513751843/pref_2 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3
subtractdbs /root/result/out9/tmp/5640223795513751843/pref_tmp_2 /root/result/out9/tmp/5640223795513751843/aln_1 /root/result/out9/tmp/5640223795513751843/pref_2 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3
Remove /root/result/out9/tmp/5640223795513751843/aln_1 ids from /root/result/out9/tmp/5640223795513751843/pref_tmp_2
[=================================================================] 1 0s 4ms
Time for merging to pref_2: 0h 0m 0s 2ms
Time for processing: 0h 0m 0s 18ms
rmdb /root/result/out9/tmp/5640223795513751843/pref_tmp_2
Time for processing: 0h 0m 0s 1ms
align /root/result/out9/tmp/5640223795513751843/profile_1 /ai/sequencedb/colabfold_db/uniref30_2302_db.idx /root/result/out9/tmp/5640223795513751843/pref_2 /root/result/out9/tmp/5640223795513751843/aln_tmp_2 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 1 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.1 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Compute score, coverage and sequence identity
Query database size: 1 type: Profile
Target database size: 36293491 type: Aminoacid
Calculation of alignments
[=================================================================] 1 0s 7ms
Time for merging to aln_tmp_2: 0h 0m 0s 0ms
7505 alignments calculated
4597 sequence pairs passed the thresholds (0.612525 of overall calculated)
4597.000000 hits per query sequence
Time for processing: 0h 0m 18s 512ms
mergedbs /root/result/out9/tmp/5640223795513751843/profile_1 /root/result/out9/res /root/result/out9/tmp/5640223795513751843/aln_1 /root/result/out9/tmp/5640223795513751843/aln_tmp_2
Merging the results to /root/result/out9/res
[=================================================================] 1 0s 1ms
Time for merging to res: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 4ms
rmdb /root/result/out9/tmp/5640223795513751843/aln_1
Time for processing: 0h 0m 0s 1ms
rmdb /root/result/out9/tmp/5640223795513751843/aln_tmp_2
Time for processing: 0h 0m 0s 1ms
mvdb /root/result/out9/tmp/latest/profile_1 /root/result/out9/prof_res
Time for processing: 0h 0m 0s 1ms
lndb /root/result/out9/qdb_h /root/result/out9/prof_res_h
Time for processing: 0h 0m 0s 1ms
expandaln /root/result/out9/qdb /ai/sequencedb/colabfold_db/uniref30_2302_db.idx /root/result/out9/res /ai/sequencedb/colabfold_db/uniref30_2302_db.idx /root/result/out9/res_exp --db-load-mode 0 --threads 64 --expansion-mode 0 -e inf --expand-filter-clusters 1 --max-seq-id 0.95
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
[=================================================================] 1 0s 8ms
Time for merging to res_exp: 0h 0m 0s 2ms
Time for processing: 0h 8m 58s 184ms
align /root/result/out9/prof_res /ai/sequencedb/colabfold_db/uniref30_2302_db.idx /root/result/out9/res_exp /root/result/out9/res_exp_realign --db-load-mode 0 -e 10 --max-accept 100000 --threads 64 --alt-ali 10 -a
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Compute score, coverage and sequence identity
Query database size: 1 type: Profile
Target database size: 350950053 type: Aminoacid
Calculation of alignments
[=================================================================] 1 0s 8ms
Time for merging to res_exp_realign: 0h 0m 0s 0ms
50815 alignments calculated
44816 sequence pairs passed the thresholds (0.881944 of overall calculated)
44816.000000 hits per query sequence
Time for processing: 0h 5m 58s 38ms
filterresult /root/result/out9/qdb /ai/sequencedb/colabfold_db/uniref30_2302_db.idx /root/result/out9/res_exp_realign /root/result/out9/res_exp_realign_filter --db-load-mode 0 --qid 0 --qsc 0.8 --diff 0 --threads 64 --max-seq-id 1.0 --filter-min-enable 100
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Query database size: 1 type: Aminoacid
Target database size: 350950053 type: Aminoacid
[=================================================================] 1 0s 5ms
Time for merging to res_exp_realign_filter: 0h 0m 0s 0ms
Time for processing: 0h 5m 47s 891ms
result2msa /root/result/out9/qdb /ai/sequencedb/colabfold_db/uniref30_2302_db.idx /root/result/out9/res_exp_realign_filter /root/result/out9/uniref.a3m --msa-format-mode 6 --db-load-mode 0 --threads 64 --filter-msa 1 --filter-min-enable 1000 --diff 3000 --qid 0.0,0.2,0.4,0.6,0.8,1.0 --qsc 0 --max-seq-id 0.95
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Query database size: 1 type: Aminoacid
Target database size: 350950053 type: Aminoacid
[=================================================================] 1 0s 5ms
Time for merging to uniref.a3m: 0h 0m 0s 0ms
Time for processing: 0h 8m 36s 437ms
rmdb /root/result/out9/res_exp_realign_filter
Time for processing: 0h 0m 0s 2ms
rmdb /root/result/out9/res_exp_realign
Time for processing: 0h 0m 0s 1ms
rmdb /root/result/out9/res_exp
Time for processing: 0h 0m 0s 3ms
rmdb /root/result/out9/res
Time for processing: 0h 0m 0s 1ms
Create directory /root/result/out9/tmp3
search /root/result/out9/prof_res /ai/sequencedb/colabfold_db/colabfold_envdb_202108_db /root/result/out9/res_env /root/result/out9/tmp3 --threads 64 --num-iterations 3 --db-load-mode 0 -a -e 0.1 --max-seqs 10000 --gpu 1 --prefilter-mode 1
ungappedprefilter /root/result/out9/prof_res /ai/sequencedb/colabfold_db/colabfold_envdb_202108_db.idx /root/result/out9/tmp3/13310131947556013529/pref_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -c 0 -e 0.1 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --min-ungapped-score 15 --max-seqs 10000 --db-load-mode 0 --gpu 1 --gpu-server 0 --gpu-server-wait-timeout 600 --prefilter-mode 1 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
[=================================================================] 1 4s 11ms
Time for merging to pref_0: 0h 0m 0s 0ms
Time for processing: 0h 1m 52s 596ms
align /root/result/out9/prof_res /ai/sequencedb/colabfold_db/colabfold_envdb_202108_db.idx /root/result/out9/tmp3/13310131947556013529/pref_0 /root/result/out9/tmp3/13310131947556013529/aln_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 1 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.1 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 1 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Compute score only
Query database size: 1 type: Profile
Target database size: 209335862 type: Aminoacid
Calculation of alignments
[=================================================================] 1 0s 7ms
Time for merging to aln_0: 0h 0m 0s 0ms
10000 alignments calculated
6989 sequence pairs passed the thresholds (0.698900 of overall calculated)
6989.000000 hits per query sequence
Time for processing: 0h 1m 41s 367ms
result2profile /root/result/out9/prof_res /ai/sequencedb/colabfold_db/colabfold_envdb_202108_db.idx /root/result/out9/tmp3/13310131947556013529/aln_0 /root/result/out9/tmp3/13310131947556013529/profile_0 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -e 0.1 --mask-profile 1 --e-profile 0.1 --comp-bias-corr 1 --comp-bias-corr-scale 1 --wg 0 --allow-deletion 0 --filter-msa 1 --filter-min-enable 0 --max-seq-id 0.9 --qid '0.0' --qsc -20 --cov 0 --diff 1000 --pseudo-cnt-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --db-load-mode 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --threads 64 --compressed 0 -v 3 --profile-output-mode 0
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Query database size: 1 type: Profile
Target database size: 209335862 type: Aminoacid
[=================================================================] 1 0s 7ms
Time for merging to profile_0: 0h 0m 0s 0ms
Time for processing: 0h 1m 39s 145ms
ungappedprefilter /root/result/out9/tmp3/13310131947556013529/profile_0 /ai/sequencedb/colabfold_db/colabfold_envdb_202108_db.idx /root/result/out9/tmp3/13310131947556013529/pref_tmp_1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -c 0 -e 0.1 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --min-ungapped-score 15 --max-seqs 10000 --db-load-mode 0 --gpu 1 --gpu-server 0 --gpu-server-wait-timeout 600 --prefilter-mode 1 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
[=================================================================] 1 4s 17ms
Time for merging to pref_tmp_1: 0h 0m 0s 0ms
Time for processing: 0h 1m 41s 808ms
subtractdbs /root/result/out9/tmp3/13310131947556013529/pref_tmp_1 /root/result/out9/tmp3/13310131947556013529/aln_0 /root/result/out9/tmp3/13310131947556013529/pref_1 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3
subtractdbs /root/result/out9/tmp3/13310131947556013529/pref_tmp_1 /root/result/out9/tmp3/13310131947556013529/aln_0 /root/result/out9/tmp3/13310131947556013529/pref_1 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3
Remove /root/result/out9/tmp3/13310131947556013529/aln_0 ids from /root/result/out9/tmp3/13310131947556013529/pref_tmp_1
[=================================================================] 1 0s 4ms
Time for merging to pref_1: 0h 0m 0s 2ms
Time for processing: 0h 0m 0s 21ms
rmdb /root/result/out9/tmp3/13310131947556013529/pref_tmp_1
Time for processing: 0h 0m 0s 1ms
align /root/result/out9/tmp3/13310131947556013529/profile_0 /ai/sequencedb/colabfold_db/colabfold_envdb_202108_db.idx /root/result/out9/tmp3/13310131947556013529/pref_1 /root/result/out9/tmp3/13310131947556013529/aln_tmp_1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 1 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.1 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Compute score, coverage and sequence identity
Query database size: 1 type: Profile
Target database size: 209335862 type: Aminoacid
Calculation of alignments
[=================================================================] 1 0s 7ms
Time for merging to aln_tmp_1: 0h 0m 0s 0ms
4099 alignments calculated
2499 sequence pairs passed the thresholds (0.609661 of overall calculated)
2499.000000 hits per query sequence
Time for processing: 0h 1m 38s 278ms
mergedbs /root/result/out9/tmp3/13310131947556013529/profile_0 /root/result/out9/tmp3/13310131947556013529/aln_1 /root/result/out9/tmp3/13310131947556013529/aln_0 /root/result/out9/tmp3/13310131947556013529/aln_tmp_1
Merging the results to /root/result/out9/tmp3/13310131947556013529/aln_1
[=================================================================] 1 0s 2ms
Time for merging to aln_1: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 7ms
rmdb /root/result/out9/tmp3/13310131947556013529/aln_0
Time for processing: 0h 0m 0s 1ms
rmdb /root/result/out9/tmp3/13310131947556013529/aln_tmp_1
Time for processing: 0h 0m 0s 1ms
result2profile /root/result/out9/tmp3/13310131947556013529/profile_0 /ai/sequencedb/colabfold_db/colabfold_envdb_202108_db.idx /root/result/out9/tmp3/13310131947556013529/aln_1 /root/result/out9/tmp3/13310131947556013529/profile_1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -e 0.1 --mask-profile 1 --e-profile 0.1 --comp-bias-corr 1 --comp-bias-corr-scale 1 --wg 0 --allow-deletion 0 --filter-msa 1 --filter-min-enable 0 --max-seq-id 0.9 --qid '0.0' --qsc -20 --cov 0 --diff 1000 --pseudo-cnt-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --db-load-mode 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --threads 64 --compressed 0 -v 3 --profile-output-mode 0
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Query database size: 1 type: Profile
Target database size: 209335862 type: Aminoacid
[=================================================================] 1 0s 7ms
Time for merging to profile_1: 0h 0m 0s 0ms
Time for processing: 0h 1m 38s 729ms
ungappedprefilter /root/result/out9/tmp3/13310131947556013529/profile_1 /ai/sequencedb/colabfold_db/colabfold_envdb_202108_db.idx /root/result/out9/tmp3/13310131947556013529/pref_tmp_2 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -c 0 -e 0.1 --cov-mode 0 --comp-bias-corr 1 --comp-bias-corr-scale 1 --min-ungapped-score 15 --max-seqs 10000 --db-load-mode 0 --gpu 1 --gpu-server 0 --gpu-server-wait-timeout 600 --prefilter-mode 1 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
[=================================================================] 1 3s 946ms
Time for merging to pref_tmp_2: 0h 0m 0s 0ms
Time for processing: 0h 1m 41s 544ms
subtractdbs /root/result/out9/tmp3/13310131947556013529/pref_tmp_2 /root/result/out9/tmp3/13310131947556013529/aln_1 /root/result/out9/tmp3/13310131947556013529/pref_2 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3
subtractdbs /root/result/out9/tmp3/13310131947556013529/pref_tmp_2 /root/result/out9/tmp3/13310131947556013529/aln_1 /root/result/out9/tmp3/13310131947556013529/pref_2 --threads 64 --e-profile 0.1 -e 0.1 --compressed 0 -v 3
Remove /root/result/out9/tmp3/13310131947556013529/aln_1 ids from /root/result/out9/tmp3/13310131947556013529/pref_tmp_2
[=================================================================] 1 0s 4ms
Time for merging to pref_2: 0h 0m 0s 2ms
Time for processing: 0h 0m 0s 23ms
rmdb /root/result/out9/tmp3/13310131947556013529/pref_tmp_2
Time for processing: 0h 0m 0s 1ms
align /root/result/out9/tmp3/13310131947556013529/profile_1 /ai/sequencedb/colabfold_db/colabfold_envdb_202108_db.idx /root/result/out9/tmp3/13310131947556013529/pref_2 /root/result/out9/tmp3/13310131947556013529/aln_tmp_2 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 1 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.1 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --comp-bias-corr-scale 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --corr-score-weight 0 --gap-open aa:11,nucl:5 --gap-extend aa:1,nucl:2 --zdrop 40 --threads 64 --compressed 0 -v 3
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Compute score, coverage and sequence identity
Query database size: 1 type: Profile
Target database size: 209335862 type: Aminoacid
Calculation of alignments
[=================================================================] 1 0s 7ms
Time for merging to aln_tmp_2: 0h 0m 0s 0ms
2222 alignments calculated
715 sequence pairs passed the thresholds (0.321782 of overall calculated)
715.000000 hits per query sequence
Time for processing: 0h 1m 36s 568ms
mergedbs /root/result/out9/tmp3/13310131947556013529/profile_1 /root/result/out9/res_env /root/result/out9/tmp3/13310131947556013529/aln_1 /root/result/out9/tmp3/13310131947556013529/aln_tmp_2
Merging the results to /root/result/out9/res_env
[=================================================================] 1 0s 2ms
Time for merging to res_env: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 6ms
rmdb /root/result/out9/tmp3/13310131947556013529/aln_1
Time for processing: 0h 0m 0s 1ms
rmdb /root/result/out9/tmp3/13310131947556013529/aln_tmp_2
Time for processing: 0h 0m 0s 1ms
expandaln /root/result/out9/prof_res /ai/sequencedb/colabfold_db/colabfold_envdb_202108_db.idx /root/result/out9/res_env /ai/sequencedb/colabfold_db/colabfold_envdb_202108_db.idx /root/result/out9/res_env_exp -e inf --expansion-mode 0 --db-load-mode 0 --threads 64
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
[=================================================================] 1 0s 25ms
Time for merging to res_env_exp: 0h 0m 0s 2ms
Time for processing: 0h 8m 38s 268ms
align /root/result/out9/tmp3/latest/profile_1 /ai/sequencedb/colabfold_db/colabfold_envdb_202108_db.idx /root/result/out9/res_env_exp /root/result/out9/res_env_exp_realign --db-load-mode 0 -e 10 --max-accept 100000 --threads 64 --alt-ali 10 -a
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Compute score, coverage and sequence identity
Query database size: 1 type: Profile
Target database size: 738695581 type: Aminoacid
Calculation of alignments
[=================================================================] 1 0s 9ms
Time for merging to res_env_exp_realign: 0h 0m 0s 0ms
78521 alignments calculated
57383 sequence pairs passed the thresholds (0.730798 of overall calculated)
57383.000000 hits per query sequence
Time for processing: 0h 6m 9s 648ms
filterresult /root/result/out9/qdb /ai/sequencedb/colabfold_db/colabfold_envdb_202108_db.idx /root/result/out9/res_env_exp_realign /root/result/out9/res_env_exp_realign_filter --db-load-mode 0 --qid 0 --qsc 0.8 --diff 0 --max-seq-id 1.0 --threads 64 --filter-min-enable 100
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Query database size: 1 type: Aminoacid
Target database size: 738695581 type: Aminoacid
[=================================================================] 1 0s 4ms
Time for merging to res_env_exp_realign_filter: 0h 0m 0s 0ms
Time for processing: 0h 6m 8s 975ms
result2msa /root/result/out9/qdb /ai/sequencedb/colabfold_db/colabfold_envdb_202108_db.idx /root/result/out9/res_env_exp_realign_filter /root/result/out9/bfd.mgnify30.metaeuk30.smag30.a3m --msa-format-mode 6 --db-load-mode 0 --threads 64 --filter-msa 1 --filter-min-enable 1000 --diff 3000 --qid 0.0,0.2,0.4,0.6,0.8,1.0 --qsc 0 --max-seq-id 0.95
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Index version: 16
Generated by: b804fbe384e6f6c9fe96322ec0e92d48bccd0a42
ScoreMatrix: VTML80.out
Query database size: 1 type: Aminoacid
Target database size: 738695581 type: Aminoacid
[=================================================================] 1 0s 5ms
Time for merging to bfd.mgnify30.metaeuk30.smag30.a3m: 0h 0m 0s 0ms
Time for processing: 0h 8m 15s 423ms
rmdb /root/result/out9/res_env_exp_realign_filter
Time for processing: 0h 0m 0s 2ms
rmdb /root/result/out9/res_env_exp_realign
Time for processing: 0h 0m 0s 1ms
rmdb /root/result/out9/res_env_exp
Time for processing: 0h 0m 0s 3ms
rmdb /root/result/out9/res_env
Time for processing: 0h 0m 0s 1ms
mergedbs /root/result/out9/qdb /root/result/out9/final.a3m /root/result/out9/uniref.a3m /root/result/out9/bfd.mgnify30.metaeuk30.smag30.a3m
Merging the results to /root/result/out9/final.a3m
[=================================================================] 1 0s 2ms
Time for merging to final.a3m: 0h 0m 0s 0ms
Time for processing: 0h 0m 0s 12ms
rmdb /root/result/out9/bfd.mgnify30.metaeuk30.smag30.a3m
Time for processing: 0h 0m 0s 1ms
rmdb /root/result/out9/uniref.a3m
Time for processing: 0h 0m 0s 1ms
unpackdb /root/result/out9/final.a3m /root/result/out9 --unpack-name-mode 0 --unpack-suffix .a3m
[=================================================================] 1 0s 8ms
Time for processing: 0h 0m 0s 20ms
rmdb /root/result/out9/final.a3m
Time for processing: 0h 0m 0s 2ms
rmdb /root/result/out9/prof_res
Time for processing: 0h 0m 0s 1ms
rmdb /root/result/out9/prof_res_h
Time for processing: 0h 0m 0s 1ms
rmdb /root/result/out9/qdb
Time for processing: 0h 0m 0s 1ms
rmdb /root/result/out9/qdb_h
Time for processing: 0h 0m 0s 1ms
My guess is that you specify db-load-mode to be 0, whereas indexes are called with 2.
The search script will actually set the parameter to the optimal value by default
In my experience it depends on how much RAM you have. Around 128GB I was able to search a query under a minute. With 64GB 12 minutes (same GPU)
--db-load-mode 2 is the option you most likely want to use for single searches. The default --db-load-mode 0 performs quite badly for single searches.
If you build the databases with MMSEQS_NO_INDEX in the setup_databases.sh script. The search script will currently force loading the whole database from disk (--db-load-mode 0) and ignore whatever was specified on the command line. You'll have to allow it to build the index, then you can use --db-load-mode 2.
I guess this is something I should revisit in the code base.