easy-predict --threads 8 /yoshitake/test/post-assemble~busco_v5/input_1/cnv2_edited.fasta /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/refseq_db_rerun.faa /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/rerun_results/cnv2_edited.fasta /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp --max-intron 130000 --max-seq-len 160000 --min-exon-aa 5 --max-overlap 5 --min-intron 1 --overlap 1 -s 6 MMseqs Version: 5.34c21f2 Substitution matrix nucl:nucleotide.out,aa:blosum62.out Add backtrace false Alignment mode 2 Alignment mode 0 Allow wrapped scoring false E-value threshold 100 Seq. id. threshold 0 Min alignment length 0 Seq. id. mode 0 Alternative alignments 0 Coverage threshold 0 Coverage mode 0 Max sequence length 160000 Compositional bias 1 Max reject 2147483647 Max accept 2147483647 Include identical seq. id. false Preload mode 0 Pseudo count a 1 Pseudo count b 1.5 Score bias 0 Realign hits false Realign score bias -0.2 Realign max seqs 2147483647 Gap open cost nucl:5,aa:11 Gap extension cost nucl:2,aa:1 Zdrop 40 Threads 8 Compressed 0 Verbosity 3 Seed substitution matrix nucl:nucleotide.out,aa:VTML80.out Sensitivity 6 k-mer length 0 k-score 2147483647 Alphabet size nucl:5,aa:21 Max results per query 300 Split database 0 Split mode 2 Split memory limit 0 Diagonal scoring true Exact k-mer matching 0 Mask residues 1 Mask lower case residues 0 Minimum diagonal score 15 Spaced k-mers 1 Spaced k-mer pattern Local temporary path Rescore mode 0 Remove hits by seq. id. and coverage false Sort results 0 Mask profile 1 Profile E-value threshold 0.001 Global sequence weighting false Allow deletions false Filter MSA 1 Maximum seq. id. threshold 0.9 Minimum seq. id. 0 Minimum score per column -20 Minimum coverage 0 Select N most diverse seqs 1000 Min codons in orf 15 Max codons in length 32734 Max orf gaps 2147483647 Contig start mode 2 Contig end mode 2 Orf start mode 1 Forward frames 1,2,3 Reverse frames 1,2,3 Translation table 1 Translate orf 0 Use all table starts false Offset of numeric ids 0 Create lookup 0 Add orf stop false Overlap between sequences 0 Sequence split mode 1 Header split mode 0 Chain overlapping alignments 0 Merge query 1 Search type 0 Search iterations 1 Start sensitivity 4 Search steps 1 Exhaustive search mode false Filter results during exhaustive search 0 Strand selection 1 LCA search mode false Disk space limit 0 MPI runner Force restart with latest tmp false Remove temporary files false maximal combined evalue of an optimal set 0.001 minimal length ratio between combined optimal set and target 0.5 Maximal intron length 130000 Minimal intron length 1 Minimal exon length aa 5 Maximal overlap of exons 5 Gap open penalty -1 Gap extend penalty -1 allow same-strand overlaps 1 translate codons to AAs 0 write target key instead of accession 0 write fragment contig coords 0 Reverse AA Fragments 0 createdb /yoshitake/test/post-assemble~busco_v5/input_1/cnv2_edited.fasta /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/contigs --dbtype 2 --compressed 0 -v 3 Converting sequences [ Time for merging to contigs_h: 0h 0m 0s 2ms Time for merging to contigs: 0h 0m 0s 39ms Database type: Nucleotide Time for processing: 0h 0m 0s 148ms createdb /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/refseq_db_rerun.faa /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/targets --dbtype 1 --compressed 0 -v 3 Converting sequences [== Time for merging to targets_h: 0h 0m 0s 6ms Time for merging to targets: 0h 0m 0s 11ms Database type: Aminoacid Time for processing: 0h 0m 0s 167ms Create directory /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict predictexons /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/contigs /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/targets /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/MetaEuk_calls /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict --sub-mat nucl:nucleotide.out,aa:blosum62.out -a 0 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 100 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 160000 --comp-bias-corr 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca 1 --pcb 1.5 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --gap-open nucl:5,aa:11 --gap-extend nucl:2,aa:1 --zdrop 40 --threads 8 --compressed 0 -v 3 --seed-sub-mat nucl:nucleotide.out,aa:VTML80.out -s 6 -k 0 --k-score 2147483647 --alph-size nucl:5,aa:21 --max-seqs 300 --split 0 --split-mode 2 --split-memory-limit 0 --diag-score 1 --exact-kmer-matching 0 --mask 1 --mask-lower-case 0 --min-ungapped-score 15 --spaced-kmer-mode 1 --rescore-mode 0 --filter-hits 0 --sort-results 0 --mask-profile 1 --e-profile 0.001 --wg 0 --allow-deletion 0 --filter-msa 1 --max-seq-id 0.9 --qid 0 --qsc -20 --cov 0 --diff 1000 --min-length 15 --max-length 32734 --max-gaps 2147483647 --contig-start-mode 2 --contig-end-mode 2 --orf-start-mode 1 --forward-frames 1,2,3 --reverse-frames 1,2,3 --translation-table 1 --translate 0 --use-all-table-starts 0 --id-offset 0 --create-lookup 0 --add-orf-stop 0 --sequence-overlap 0 --sequence-split-mode 1 --headers-split-mode 0 --chain-alignments 0 --merge-query 1 --search-type 0 --num-iterations 1 --start-sens 4 --sens-steps 1 --exhaustive-search 0 --exhaustive-search-filter 0 --strand 1 --lca-search 0 --disk-space-limit 0 --force-reuse 0 --remove-tmp-files 0 --metaeuk-eval 0.001 --metaeuk-tcov 0.5 --max-intron 130000 --min-intron 1 --min-exon-aa 5 --max-overlap 5 --set-gap-open -1 --set-gap-extend -1 --reverse-fragments 0 extractorfs /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/contigs /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/nucl_6f --min-length 15 --max-length 32734 --max-gaps 2147483647 --contig-start-mode 2 --contig-end-mode 2 --orf-start-mode 1 --forward-frames 1,2,3 --reverse-frames 1,2,3 --translation-table 1 --translate 0 --use-all-table-starts 0 --id-offset 0 --create-lookup 0 --threads 8 --compressed 0 -v 3 [=================================================================] 184 0s 362ms Time for merging to nucl_6f_h: 0h 0m 0s 323ms Time for merging to nucl_6f: 0h 0m 0s 522ms Time for processing: 0h 0m 1s 950ms translatenucs /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/nucl_6f /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/aa_6f --translation-table 1 --add-orf-stop 0 -v 3 --compressed 0 --threads 8 [=================================================================] 1.91M 0s 463ms Time for merging to aa_6f: 0h 0m 0s 668ms Time for processing: 0h 0m 1s 279ms Create directory /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/tmp_search search /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/aa_6f /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/targets /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/search_res /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/tmp_search --sub-mat nucl:nucleotide.out,aa:blosum62.out -a 0 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 100 --min-seq-id 0 --min-aln-len 5 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 160000 --comp-bias-corr 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca 1 --pcb 1.5 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --gap-open nucl:5,aa:11 --gap-extend nucl:2,aa:1 --zdrop 40 --threads 8 --compressed 0 -v 3 --seed-sub-mat nucl:nucleotide.out,aa:VTML80.out -s 6 -k 0 --k-score 2147483647 --alph-size nucl:5,aa:21 --max-seqs 300 --split 0 --split-mode 2 --split-memory-limit 0 --diag-score 1 --exact-kmer-matching 0 --mask 1 --mask-lower-case 0 --min-ungapped-score 15 --spaced-kmer-mode 1 --rescore-mode 0 --filter-hits 0 --sort-results 0 --mask-profile 1 --e-profile 0.001 --wg 0 --allow-deletion 0 --filter-msa 1 --max-seq-id 0.9 --qid 0 --qsc -20 --cov 0 --diff 1000 --min-length 15 --max-length 32734 --max-gaps 2147483647 --contig-start-mode 2 --contig-end-mode 2 --orf-start-mode 1 --forward-frames 1,2,3 --reverse-frames 1,2,3 --translation-table 1 --translate 0 --use-all-table-starts 0 --id-offset 0 --create-lookup 0 --add-orf-stop 0 --sequence-overlap 0 --sequence-split-mode 1 --headers-split-mode 0 --chain-alignments 0 --merge-query 1 --search-type 0 --num-iterations 1 --start-sens 4 --sens-steps 1 --exhaustive-search 0 --exhaustive-search-filter 0 --strand 1 --lca-search 0 --disk-space-limit 0 --force-reuse 0 --remove-tmp-files 0 prefilter /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/aa_6f /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/targets /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/tmp_search/14565432346859506782/pref_0 --sub-mat nucl:nucleotide.out,aa:blosum62.out --seed-sub-mat nucl:nucleotide.out,aa:VTML80.out -k 0 --k-score 2147483647 --alph-size nucl:5,aa:21 --max-seq-len 160000 --max-seqs 300 --split 0 --split-mode 2 --split-memory-limit 0 -c 0 --cov-mode 0 --comp-bias-corr 1 --diag-score 1 --exact-kmer-matching 0 --mask 1 --mask-lower-case 0 --min-ungapped-score 15 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca 1 --pcb 1.5 --threads 8 --compressed 0 -v 3 -s 6.0 Query database size: 1905846 type: Aminoacid Estimated memory consumption: 1G Target database size: 26961 type: Aminoacid Index table k-mer threshold: 109 at k-mer size 6 Index table: counting k-mers [=================================================================] 26.96K 0s 370ms Index table: Masked residues: 97089 Index table: fill [=================================================================] 26.96K 0s 258ms Index statistics Entries: 8657649 DB size: 537 MB Avg k-mer size: 0.135276 Top 10 k-mers IEFWSG 1164 NGITNL 1146 MLASYK 1058 LIGPKV 1052 NMYCLY 1007 SDTSLY 966 SMLLFY 846 LNFTDQ 802 SKYFEM 794 DTGIFT 790 Time for index table init: 0h 0m 0s 996ms Process prefiltering step 1 of 1 k-mer similarity threshold: 109 Starting prefiltering scores calculation (step 1 of 1) Query db start 1 to 1905846 Target db start 1 to 26961 [=================================================================] 1.91M 2m 26s 356ms 352.033339 k-mers per position 1480 DB matches per sequence 0 overflows 0 queries produce too many hits (truncated result) 12 sequences passed prefiltering per query sequence 4 median result list length 366265 sequences with 0 size result lists Time for merging to pref_0: 0h 0m 0s 604ms Time for processing: 0h 2m 29s 947ms align /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/aa_6f /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/targets /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/tmp_search/14565432346859506782/pref_0 /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/search_res --sub-mat nucl:nucleotide.out,aa:blosum62.out -a 0 --alignment-mode 2 --alignment-output-mode 0 --wrapped-scoring 0 -e 100 --min-seq-id 0 --min-aln-len 5 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 160000 --comp-bias-corr 1 --max-rejected 2147483647 --max-accept 2147483647 --add-self-matches 0 --db-load-mode 0 --pca 1 --pcb 1.5 --score-bias 0 --realign 0 --realign-score-bias -0.2 --realign-max-seqs 2147483647 --gap-open nucl:5,aa:11 --gap-extend nucl:2,aa:1 --zdrop 40 --threads 8 --compressed 0 -v 3 Compute score and coverage Query database size: 1905846 type: Aminoacid Target database size: 26961 type: Aminoacid Calculation of alignments [=================================================================] 1.91M 57s 907ms Time for merging to search_res: 0h 0m 0s 598ms 22909454 alignments calculated 3704627 sequence pairs passed the thresholds (0.161707 of overall calculated) 1.943823 hits per query sequence Time for processing: 0h 0m 58s 828ms resultspercontig /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/contigs /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/nucl_6f /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/search_res /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/search_res_by_contig --threads 8 --compressed 0 -v 3 Computing ORF lookup Computing contig offsets Computing contig lookup Time for contig lookup: 0h 0m 0s 99ms ==[===============================================================] 184 2s 546ms Time for merging to search_res_by_contig: 0h 0m 0s 0ms Time for processing: 0h 0m 2s 961ms collectoptimalset /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/search_res_by_contig /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/targets /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/dp_predictions --metaeuk-eval 0.001 --metaeuk-tcov 0.5 --max-intron 130000 --min-intron 1 --min-exon-aa 5 --max-overlap 5 --set-gap-open -1 --set-gap-extend -1 --score-bias 0 --threads 8 --compressed 0 -v 3 [=================================================================] 184 1s 388ms Time for merging to dp_predictions: 0h 0m 0s 2ms Time for processing: 0h 0m 1s 414ms mvdb /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/tmp_predict/12270607685310061161/dp_predictions /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/MetaEuk_calls Time for processing: 0h 0m 0s 0ms reduceredundancy /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/MetaEuk_calls /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/MetaEuk_preds /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/MetaEuk_preds_clust --overlap 1 --threads 8 --compressed 0 -v 3 [=================================================================] 184 0s 22ms Time for merging to MetaEuk_preds_clust: 0h 0m 0s 0ms Time for merging to MetaEuk_preds: 0h 0m 0s 0ms Time for processing: 0h 0m 0s 32ms unitesetstofasta /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/contigs /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/targets /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/tmp/1551443308695284391/MetaEuk_preds /yoshitake/test/post-assemble~busco_v5/cnv2_edited.fasta.busco/run_eukaryota_odb10/metaeuk_output/rerun_results/cnv2_edited.fasta --protein 0 --translation-table 1 --target-key 0 --write-frag-coords 0 --max-seq-len 160000 --threads 8 -v 3 [=================================================================] 184 0s 6ms Time for merging to cnv2_edited.fasta.fas: 0h 0m 0s 1ms Time for merging to cnv2_edited.fasta.codon.fas: 0h 0m 0s 1ms Time for merging to cnv2_edited.fasta.headersMap.tsv: 0h 0m 0s 0ms Time for merging to cnv2_edited.fasta.gff: 0h 0m 0s 0ms Time for processing: 0h 0m 0s 22ms