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MMseqs cluster : Invalid database read ... Error: Offset step died #830

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actledge opened this issue Mar 29, 2024 · 0 comments
Open

MMseqs cluster : Invalid database read ... Error: Offset step died #830

actledge opened this issue Mar 29, 2024 · 0 comments

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@actledge
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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

Your Environment

Include as many relevant details about the environment you experienced the bug in.

  • Git commit used (The string after "MMseqs Version:" when you execute MMseqs without any parameters): MMseqs2 Version: 15.6f452
  • Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.): latest 15.6f452 installed by conda
  • Server specifications (especially CPU support for AVX2/SSE and amount of system memory): 1T memory
  • Operating system and version: CentOS
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@actledge