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soedinglab / MMseqs2

MMseqs2: ultra fast and sensitive search and clustering suite
https://mmseqs.com
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MMseqs cluster : Invalid database read ... Error: Offset step died #830

Open actledge opened 6 months ago

actledge commented 6 months ago

My command:

mmseqs createdb 1831648_seqs.fasta 1831648_seqs.mmseqs2db
mmseqs cluster 1831648_seqs.mmseqs2db 1831648_seqs.mmseqs2clu tmp --cov-mode 0 -c 0.85 --min-seq-id 0.95 --threads 112

My fasta file have 1.8 million sequences, and the size is about 30G.

MMseqs Output (for bugs)

Create directory tmp cluster 1831648_seqs.mmseqs2db 1831648_seqs.mmseqs2clu tmp --cov-mode 0 -c 0.85 --min-seq-id 0.95 --threads 112

MMseqs Version: 15.6f452 Substitution matrix aa:blosum62.out,nucl:nucleotide.out Seed substitution matrix aa:VTML80.out,nucl:nucleotide.out Sensitivity 4 k-mer length 15 Target search mode 0 k-score seq:2147483647,prof:2147483647 Alphabet size aa:21,nucl:5 Max sequence length 10000 Max results per query 20 Split database 0 Split mode 2 Split memory limit 0 Coverage threshold 0.85 Coverage mode 0 Compositional bias 1 Compositional bias 1 Diagonal scoring false Exact k-mer matching 1 Mask residues 1 Mask residues probability 0.9 Mask lower case residues 0 Minimum diagonal score 15 Selected taxa
Include identical seq. id. false Spaced k-mers 1 Preload mode 0 Pseudo count a substitution:1.100,context:1.400 Pseudo count b substitution:4.100,context:5.800 Spaced k-mer pattern
Local temporary path
Threads 112 Compressed 0 Verbosity 3 Add backtrace false Alignment mode 3 Alignment mode 0 Allow wrapped scoring false E-value threshold 0.001 Seq. id. threshold 0.95 Min alignment length 0 Seq. id. mode 0 Alternative alignments 0 Max reject 2147483647 Max accept 2147483647 Score bias 0 Realign hits false Realign score bias -0.2 Realign max seqs 2147483647 Correlation score weight 0 Gap open cost aa:11,nucl:5 Gap extension cost aa:1,nucl:2 Zdrop 40 Rescore mode 0 Remove hits by seq. id. and coverage false Sort results 0 Cluster mode 0 Max connected component depth 1000 Similarity type 2 Weight file name
Cluster Weight threshold 0.9 Single step clustering false Cascaded clustering steps 3 Cluster reassign false Remove temporary files false Force restart with latest tmp false MPI runner
k-mers per sequence 21 Scale k-mers per sequence aa:0.000,nucl:0.200 Adjust k-mer length false Shift hash 67 Include only extendable false Skip repeating k-mers false

Set cluster sensitivity to -s 1.000000 Set cluster mode SET COVER Set cluster iterations to 1 linclust 1831648_seqs.mmseqs2db tmp/16479300059278292880/clu_redundancy tmp/16479300059278292880/linclust --cluster-mode 0 --max-iterations 1000 --similarity-type 2 --threads 112 --compressed 0 -v 3 --cluster-weight-threshold 0.9 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.001 --min-seq-id 0.95 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.85 --cov-mode 0 --max-seq-len 10000 --comp-bias-corr 0 --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 --alph-size aa:21,nucl:5 --kmer-per-seq 21 --spaced-kmer-mode 1 --kmer-per-seq-scale aa:0.000,nucl:0.200 --adjust-kmer-len 0 --mask 1 --mask-prob 0.9 --mask-lower-case 0 -k 0 --hash-shift 67 --split-memory-limit 0 --include-only-extendable 0 --ignore-multi-kmer 0 --rescore-mode 0 --filter-hits 0 --sort-results 0 --remove-tmp-files 0 --force-reuse 0

kmermatcher 1831648_seqs.mmseqs2db tmp/16479300059278292880/linclust/10067396915876818640/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:21,nucl:5 --min-seq-id 0.95 --kmer-per-seq 21 --spaced-kmer-mode 1 --kmer-per-seq-scale aa:0.000,nucl:0.200 --adjust-kmer-len 0 --mask 1 --mask-prob 0.9 --mask-lower-case 0 --cov-mode 0 -k 0 -c 0.85 --max-seq-len 10000 --hash-shift 67 --split-memory-limit 0 --include-only-extendable 0 --ignore-multi-kmer 0 --threads 112 --compressed 0 -v 3 --cluster-weight-threshold 0.9

kmermatcher 1831648_seqs.mmseqs2db tmp/16479300059278292880/linclust/10067396915876818640/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --alph-size aa:21,nucl:5 --min-seq-id 0.95 --kmer-per-seq 21 --spaced-kmer-mode 1 --kmer-per-seq-scale aa:0.000,nucl:0.200 --adjust-kmer-len 0 --mask 1 --mask-prob 0.9 --mask-lower-case 0 --cov-mode 0 -k 0 -c 0.85 --max-seq-len 10000 --hash-shift 67 --split-memory-limit 0 --include-only-extendable 0 --ignore-multi-kmer 0 --threads 112 --compressed 0 -v 3 --cluster-weight-threshold 0.9

Database size: 1831648 type: Nucleotide

Generate k-mers list for 1 split [=================================================================] 1.83M 2m 36s 559ms

Adjusted k-mer length 17 Sort kmer 0h 0m 33s 753ms Sort by rep. sequence 0h 0m 2s 503ms Time for fill: 0h 0m 4s 992ms Time for merging to pref: 0h 0m 0s 10ms Time for processing: 0h 4m 21s 927ms rescorediagonal 1831648_seqs.mmseqs2db 1831648_seqs.mmseqs2db tmp/16479300059278292880/linclust/10067396915876818640/pref tmp/16479300059278292880/linclust/10067396915876818640/pref_rescore1 --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --rescore-mode 0 --wrapped-scoring 0 --filter-hits 0 -e 0.001 -c 0.85 -a 0 --cov-mode 0 --min-seq-id 0.95 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 112 --compressed 0 -v 3

[=================================================================] 1.83M 10s 370ms Time for merging to pref_rescore1: 0h 0m 0s 781ms Time for processing: 0h 0m 21s 118ms clust 1831648_seqs.mmseqs2db tmp/16479300059278292880/linclust/10067396915876818640/pref_rescore1 tmp/16479300059278292880/linclust/10067396915876818640/pre_clust --cluster-mode 0 --max-iterations 1000 --similarity-type 2 --threads 112 --compressed 0 -v 3 --cluster-weight-threshold 0.9

Clustering mode: Set Cover [=================================================================] 1.83M 0s 184ms Sort entries Find missing connections Found 1239487 new connections. Reconstruct initial order [=================================================================] 1.83M 0s 214ms Add missing connections [=================================================================] 1.83M 0s 85ms

Time for read in: 0h 0m 1s 30ms Total time: 0h 0m 1s 209ms

Size of the sequence database: 1831648 Size of the alignment database: 1831648 Number of clusters: 855530

Writing results 0h 0m 0s 123ms Time for merging to pre_clust: 0h 0m 0s 5ms Time for processing: 0h 0m 1s 753ms createsubdb tmp/16479300059278292880/linclust/10067396915876818640/order_redundancy 1831648_seqs.mmseqs2db tmp/16479300059278292880/linclust/10067396915876818640/input_step_redundancy -v 3 --subdb-mode 1

Time for merging to input_step_redundancy: 0h 0m 0s 6ms Time for processing: 0h 0m 0s 308ms createsubdb tmp/16479300059278292880/linclust/10067396915876818640/order_redundancy tmp/16479300059278292880/linclust/10067396915876818640/pref tmp/16479300059278292880/linclust/10067396915876818640/pref_filter1 -v 3 --subdb-mode 1

Time for merging to pref_filter1: 0h 0m 0s 16ms Time for processing: 0h 0m 0s 564ms filterdb tmp/16479300059278292880/linclust/10067396915876818640/pref_filter1 tmp/16479300059278292880/linclust/10067396915876818640/pref_filter2 --filter-file tmp/16479300059278292880/linclust/10067396915876818640/order_redundancy --threads 112 --compressed 0 -v 3

Filtering using file(s) [=================================================================] 855.53K 0s 584ms Time for merging to pref_filter2: 0h 0m 1s 180ms Time for processing: 0h 0m 3s 237ms align tmp/16479300059278292880/linclust/10067396915876818640/input_step_redundancy tmp/16479300059278292880/linclust/10067396915876818640/input_step_redundancy tmp/16479300059278292880/linclust/10067396915876818640/pref_filter2 tmp/16479300059278292880/linclust/10067396915876818640/aln --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.001 --min-seq-id 0.95 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.85 --cov-mode 0 --max-seq-len 10000 --comp-bias-corr 0 --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 112 --compressed 0 -v 3

Compute score, coverage and sequence identity Query database size: 855530 type: Nucleotide Target database size: 855530 type: Nucleotide Calculation of alignments [=================================================================] 855.53K 2m 53s 344ms Time for merging to aln: 0h 0m 0s 811ms 12214778 alignments calculated 932129 sequence pairs passed the thresholds (0.076312 of overall calculated) 1.089534 hits per query sequence Time for processing: 0h 3m 4s 809ms clust tmp/16479300059278292880/linclust/10067396915876818640/input_step_redundancy tmp/16479300059278292880/linclust/10067396915876818640/aln tmp/16479300059278292880/linclust/10067396915876818640/clust --cluster-mode 0 --max-iterations 1000 --similarity-type 2 --threads 112 --compressed 0 -v 3 --cluster-weight-threshold 0.9

Clustering mode: Set Cover [=================================================================] 855.53K 0s 54ms Sort entries Find missing connections Found 76599 new connections. Reconstruct initial order [=================================================================] 855.53K 0s 78ms Add missing connections [=================================================================] 855.53K 0s 44ms

Time for read in: 0h 0m 0s 583ms Total time: 0h 0m 0s 671ms

Size of the sequence database: 855530 Size of the alignment database: 855530 Number of clusters: 802273

Writing results 0h 0m 0s 99ms Time for merging to clust: 0h 0m 0s 8ms Time for processing: 0h 0m 1s 85ms mergeclusters 1831648_seqs.mmseqs2db tmp/16479300059278292880/clu_redundancy tmp/16479300059278292880/linclust/10067396915876818640/pre_clust tmp/16479300059278292880/linclust/10067396915876818640/clust --threads 112 --compressed 0 -v 3

Clustering step 1 [=================================================================] 855.53K 0s 687ms Clustering step 2 [=================================================================] 802.27K 0s 949ms Write merged clustering [=================================================================] 1.83M 1s 694ms Time for merging to clu_redundancy: 0h 0m 0s 935ms Time for processing: 0h 0m 3s 228ms createsubdb tmp/16479300059278292880/clu_redundancy 1831648_seqs.mmseqs2db tmp/16479300059278292880/input_step_redundancy -v 3 --subdb-mode 1

Time for merging to input_step_redundancy: 0h 0m 0s 12ms Time for processing: 0h 0m 0s 479ms extractframes tmp/16479300059278292880/input_step_redundancy tmp/16479300059278292880/query_seqs --forward-frames 1 --reverse-frames 1 --create-lookup 0 --threads 112 --compressed 0 -v 3

[=================================================================] 802.27K 9s 504ms Time for merging to query_seqs_h: 0h 0m 0s 682ms Time for merging to query_seqs: 0h 0m 38s 582ms Time for processing: 0h 0m 52s 983ms prefilter tmp/16479300059278292880/query_seqs tmp/16479300059278292880/input_step_redundancy tmp/16479300059278292880/pref --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --seed-sub-mat 'aa:VTML80.out,nucl:nucleotide.out' -s 1 -k 15 --target-search-mode 0 --k-score seq:2147483647,prof:2147483647 --alph-size aa:21,nucl:5 --max-seq-len 10000 --max-seqs 300 --split 0 --split-mode 2 --split-memory-limit 0 -c 0.85 --cov-mode 0 --comp-bias-corr 0 --comp-bias-corr-scale 1 --diag-score 0 --exact-kmer-matching 1 --mask 1 --mask-prob 0.9 --mask-lower-case 0 --min-ungapped-score 60 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca substitution:1.100,context:1.400 --pcb substitution:4.100,context:5.800 --threads 112 --compressed 0 -v 3

Query database size: 1604546 type: Nucleotide Estimated memory consumption: 105G Target database size: 802273 type: Nucleotide Index table k-mer threshold: 0 at k-mer size 15 Index table: counting k-mers [=================================================================] 802.27K 1m 13s 891ms Index table: Masked residues: 47468793 Index table: fill [=================================================================] 802.27K 1m 7s 245ms Index statistics Entries: 14067080711 DB size: 88684 MB Avg k-mer size: 13.100990 Top 10 k-mers CCCTCGCAAGGTTAC 15119 TGGGATCCCCGGGGG 14445 GGTCGGGTCCCGTAG 12691 GGTATCCCCTCGAGG 12523 CATAAAAACCGAGGG 12298 TAAAAACCCCGGGGG 12038 TTTTATTTTATTCTT 9764 CTTAGGGGTTACGTT 9670 GTGTAATCCCTCGAG 9663 CTGAAACCATTCTCG 9602 Time for index table init: 0h 2m 35s 948ms Process prefiltering step 1 of 1

k-mer similarity threshold: 0 Starting prefiltering scores calculation (step 1 of 1) Query db start 1 to 1604546 Target db start 1 to 802273 [=================================================================] 1.60M 1h 46m 59s 76ms

0.996125 k-mers per position 14106896 DB matches per sequence 1161942 overflows 277 sequences passed prefiltering per query sequence 300 median result list length 3973 sequences with 0 size result lists Time for merging to pref: 0h 0m 0s 974ms Time for processing: 1h 49m 41s 539ms rescorediagonal tmp/16479300059278292880/query_seqs tmp/16479300059278292880/input_step_redundancy tmp/16479300059278292880/pref tmp/16479300059278292880/aln_ungapped --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' --rescore-mode 2 --wrapped-scoring 0 --filter-hits 0 -e 0.001 -c 0.85 -a 0 --cov-mode 0 --min-seq-id 0.95 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 112 --compressed 0 -v 3

[=================================================================] 1.60M 14m 50s 51ms Time for merging to aln_ungapped: 0h 0m 1s 439ms Time for processing: 0h 15m 7s 16ms subtractdbs tmp/16479300059278292880/pref tmp/16479300059278292880/aln_ungapped tmp/16479300059278292880/pref_subtract --threads 112 --compressed 0 -v 3

subtractdbs tmp/16479300059278292880/pref tmp/16479300059278292880/aln_ungapped tmp/16479300059278292880/pref_subtract --threads 112 --compressed 0 -v 3

Remove tmp/16479300059278292880/aln_ungapped ids from tmp/16479300059278292880/pref [=================================================================] 1.60M 1s 175ms Time for merging to pref_subtract: 0h 0m 1s 400ms Time for processing: 0h 0m 5s 506ms align tmp/16479300059278292880/query_seqs tmp/16479300059278292880/input_step_redundancy tmp/16479300059278292880/pref_subtract tmp/16479300059278292880/aln_gapped --sub-mat 'aa:blosum62.out,nucl:nucleotide.out' -a 0 --alignment-mode 3 --alignment-output-mode 0 --wrapped-scoring 0 -e 0.001 --min-seq-id 0.95 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0.85 --cov-mode 0 --max-seq-len 10000 --comp-bias-corr 0 --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 112 --compressed 0 -v 3

Compute score, coverage and sequence identity Query database size: 1604546 type: Nucleotide Target database size: 802273 type: Nucleotide Calculation of alignments [=================================================================] 1.60M 22m 53s 435ms Time for merging to aln_gapped: 0h 0m 0s 903ms 70826259 alignments calculated 3445894 sequence pairs passed the thresholds (0.048653 of overall calculated) 2.147582 hits per query sequence Time for processing: 0h 23m 4s 596ms concatdbs tmp/16479300059278292880/aln_ungapped tmp/16479300059278292880/aln_gapped tmp/16479300059278292880/aln --preserve-keys --take-larger-entry --threads 112 --compressed 0 -v 3

[=================================================================] 1.60M 0s 217ms [=================================================================] 1.60M 0s 385ms Time for merging to aln: 0h 0m 1s 623ms Time for processing: 0h 0m 3s 354ms offsetalignment tmp/16479300059278292880/input_step_redundancy tmp/16479300059278292880/query_seqs tmp/16479300059278292880/input_step_redundancy tmp/16479300059278292880/input_step_redundancy tmp/16479300059278292880/aln tmp/16479300059278292880/aln_off --chain-alignments 0 --merge-query 1 --search-type 3 --threads 112 --compressed 0 --db-load-mode 0 -v 3

Computing ORF lookup Computing contig offsets Computing contig lookup Time for contig lookup: 0h 0m 0s 560ms Writing results to: tmp/16479300059278292880/aln_off [Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Invalid database read for id=4294967295, database index=tmp/16479300059278292880/input_step_redundancy.index getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) getSeqLen: local id (4294967295) >= db size (802273) Error: Offset step died

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zhongguojie1998 commented 2 months ago

Hi mmseqs2 team. I got a similar issue when using mmseqs easy-cluster. My database has about 80M sequences. It seems only happen on large databases. Could you please check this issue? Thanks a lot.