Tmp tmp folder does not exist or is not a directory.
Shuffle database can not be combined with --createdb-mode 0.
We recompute with --shuffle 0.
Converting sequences
[========================================================================
Time for merging to input_h: 0h 0m 0s 238ms
Time for merging to input: 0h 0m 0s 231ms
Database type: Nucleotide
Time for merging to input.lookup: 0h 0m 0s 14ms
Time for processing: 0h 0m 13s 347ms
Tmp tmp/400274352841473142/clu_tmp folder does not exist or is not a directory.
kmermatcher tmp/400274352841473142/input tmp/400274352841473142/clu_tmp/6471805245930475850/pref --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.99 --kmer-per-seq 21 --kmer-per-seq-scale 0.4 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 1 -k 0 -c 1 --max-seq-len 65535 --hash-shift 5 --split-memory-limit 0 --include-only-extendable 0 --ignore-multi-kmer 0 --threads 40 --compressed 0 -v 3 

kmermatcher tmp/400274352841473142/input tmp/400274352841473142/clu_tmp/6471805245930475850/pref --sub-mat nucl:nucleotide.out,aa:blosum62.out --alph-size 13 --min-seq-id 0.99 --kmer-per-seq 21 --kmer-per-seq-scale 0.4 --adjust-kmer-len 0 --mask 0 --mask-lower-case 0 --cov-mode 1 -k 0 -c 1 --max-seq-len 65535 --hash-shift 5 --split-memory-limit 0 --include-only-extendable 0 --ignore-multi-kmer 0 --threads 40 --compressed 0 -v 3 

Database size: 724578 type: Nucleotide

Estimated memory consumption 91743 MB
Generate k-mers list for 1 split
[=================================================================] 724.58K 1m 17s 548ms

Adjusted k-mer length 16
Sort kmer 0h 2m 48s 470ms
Sort by rep. sequence 0h 2m 21s 225ms
Time for fill: 0h 2m 27s 262ms
Time for merging to pref: 0h 0m 0s 276ms
Time for processing: 0h 15m 26s 78ms
rescorediagonal tmp/400274352841473142/input tmp/400274352841473142/input tmp/400274352841473142/clu_tmp/6471805245930475850/pref tmp/400274352841473142/clu_tmp/6471805245930475850/pref_rescore1 --sub-mat nucl:nucleotide.out,aa:blosum62.out --rescore-mode 0 --wrapped-scoring 0 --filter-hits 0 -e 0.001 -c 1 -a 0 --cov-mode 1 --min-seq-id 0.99 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 40 --compressed 0 -v 3 

[=================================================================] 724.58K 13m 35s 885ms
Time for merging to pref_rescore1: 0h 0m 0s 559ms
Time for processing: 0h 13m 48s 162ms
clust tmp/400274352841473142/input tmp/400274352841473142/clu_tmp/6471805245930475850/pref_rescore1 tmp/400274352841473142/clu_tmp/6471805245930475850/pre_clust --cluster-mode 3 --max-iterations 1000 --similarity-type 2 --threads 40 --compressed 0 -v 3 

Clustering mode: Greedy Low Mem
Total time: 0h 0m 0s 129ms

Size of the sequence database: 724578
Size of the alignment database: 724578
Number of clusters: 558200

Writing results 0h 0m 0s 154ms
Time for merging to pre_clust: 0h 0m 0s 186ms
Time for processing: 0h 0m 0s 751ms
createsubdb tmp/400274352841473142/clu_tmp/6471805245930475850/order_redundancy tmp/400274352841473142/input tmp/400274352841473142/clu_tmp/6471805245930475850/input_step_redundancy -v 3 --subdb-mode 1 

Time for merging to input_step_redundancy: 0h 0m 0s 305ms
Time for processing: 0h 0m 0s 567ms
createsubdb tmp/400274352841473142/clu_tmp/6471805245930475850/order_redundancy tmp/400274352841473142/clu_tmp/6471805245930475850/pref tmp/400274352841473142/clu_tmp/6471805245930475850/pref_filter1 -v 3 --subdb-mode 1 

Time for merging to pref_filter1: 0h 0m 0s 206ms
Time for processing: 0h 0m 0s 439ms
filterdb tmp/400274352841473142/clu_tmp/6471805245930475850/pref_filter1 tmp/400274352841473142/clu_tmp/6471805245930475850/pref_filter2 --filter-file tmp/400274352841473142/clu_tmp/6471805245930475850/order_redundancy 

Filtering using file(s)
[=================================================================] 558.20K 44s 593ms
Time for merging to pref_filter2: 0h 0m 2s 87ms
Time for processing: 0h 6m 20s 206ms
align tmp/400274352841473142/clu_tmp/6471805245930475850/input_step_redundancy tmp/400274352841473142/clu_tmp/6471805245930475850/input_step_redundancy tmp/400274352841473142/clu_tmp/6471805245930475850/pref_filter2 tmp/400274352841473142/clu_tmp/6471805245930475850/aln --sub-mat nucl:nucleotide.out,aa:blosum62.out -a 0 --alignment-mode 2 --wrapped-scoring 0 -e 0.001 --min-seq-id 0.99 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 1 --cov-mode 1 --max-seq-len 65535 --comp-bias-corr 1 --realign 0 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca 1 --pcb 1.5 --score-bias 0 --gap-open 11 --gap-extend 1 --threads 40 --compressed 0 -v 3 

Compute score and coverage
Query database size: 558200 type: Nucleotide
Target database size: 558200 type: Nucleotide
Calculation of alignments
[=================================================================] 558.20K 1h 53m 37s 28ms
Time for merging to aln: 0h 0m 0s 443ms

1933544554 alignments calculated.
594792 sequence pairs passed the thresholds (0.000308 of overall calculated).
1.065554 hits per query sequence.
Time for processing: 1h 53m 53s 155ms
clust tmp/400274352841473142/clu_tmp/6471805245930475850/input_step_redundancy tmp/400274352841473142/clu_tmp/6471805245930475850/aln tmp/400274352841473142/clu_tmp/6471805245930475850/clust --cluster-mode 3 --max-iterations 1000 --similarity-type 2 --threads 40 --compressed 0 -v 3 

Clustering mode: Greedy Low Mem
Total time: 0h 0m 0s 95ms

Size of the sequence database: 558200
Size of the alignment database: 558200
Number of clusters: 528847

Writing results 0h 0m 0s 117ms
Time for merging to clust: 0h 0m 0s 781ms
Time for processing: 0h 0m 1s 234ms
mergeclusters tmp/400274352841473142/input tmp/400274352841473142/clu tmp/400274352841473142/clu_tmp/6471805245930475850/pre_clust tmp/400274352841473142/clu_tmp/6471805245930475850/clust --threads 40 --compressed 0 -v 3 

Clustering step 1
[=================================================================] 558.20K 0s 249ms
Clustering step 2
[=================================================================] 528.85K 0s 414ms
Write merged clustering
[=================================================================] 724.58K 0s 696ms
Time for merging to clu: 0h 0m 0s 386ms
Time for processing: 0h 0m 1s 445ms
Remove temporary files
rmdb tmp/400274352841473142/clu_tmp/6471805245930475850/pref 

Time for processing: 0h 0m 4s 287ms
rmdb tmp/400274352841473142/clu_tmp/6471805245930475850/pref_rescore1 

Time for processing: 0h 0m 0s 244ms
rmdb tmp/400274352841473142/clu_tmp/6471805245930475850/pre_clust 

Time for processing: 0h 0m 0s 20ms
rmdb tmp/400274352841473142/clu_tmp/6471805245930475850/input_step_redundancy 

Time for processing: 0h 0m 0s 40ms
rmdb tmp/400274352841473142/clu_tmp/6471805245930475850/pref_filter1 

Time for processing: 0h 0m 0s 16ms
rmdb tmp/400274352841473142/clu_tmp/6471805245930475850/pref_filter2 

Time for processing: 0h 0m 3s 4ms
rmdb tmp/400274352841473142/clu_tmp/6471805245930475850/clust 

Time for processing: 0h 0m 0s 19ms
createtsv tmp/400274352841473142/input tmp/400274352841473142/input tmp/400274352841473142/clu tmp/400274352841473142/cluster.tsv --threads 40 -v 3 

Time for merging to cluster.tsv: 0h 0m 1s 351ms
Time for processing: 0h 0m 7s 330ms
result2repseq tmp/400274352841473142/input tmp/400274352841473142/clu tmp/400274352841473142/clu_rep --threads 40 -v 3 

[=================================================================] 528.85K 0s 823ms
Time for merging to clu_rep: 0h 2m 7s 661ms
Time for processing: 0h 3m 45s 102ms
Error: result2flat died