Created
April 4, 2021 18:07
-
-
Save genomewalker/e5b05deb965660e275a39a8153dab9e9 to your computer and use it in GitHub Desktop.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| easy-taxonomy e77760e07c3167ef94f937365175d68b.assm.combined.fasta DB/uniref50-tax/UniRef50 e77760e07c3167ef94f937365175d68b.UniRef50 /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50 --tax-lineage 2 --majority 0.5 --vote-mode 1 --lca-mode 3 --orf-filter 1 --lca-ranks superkingdom,phylum,class,order,family,genus --threads 32 | |
| MMseqs Version: 5daca424b162cc5fdf0b9cd151aebed86975cbf6 | |
| ORF filter 1 | |
| ORF filter e-value 100 | |
| ORF filter sensitivity 2 | |
| LCA mode 3 | |
| Majority threshold 0.5 | |
| Vote mode 1 | |
| LCA ranks superkingdom,phylum,class,order,family,genus | |
| Column with taxonomic lineage 2 | |
| Compressed 0 | |
| Threads 32 | |
| Verbosity 3 | |
| Taxon blacklist 12908:unclassified sequences,28384:other sequences | |
| Substitution matrix nucl:nucleotide.out,aa:blosum62.out | |
| Add backtrace false | |
| Alignment mode 0 | |
| Alignment mode 0 | |
| Allow wrapped scoring false | |
| E-value threshold 0.001 | |
| Seq. id. threshold 0 | |
| Min alignment length 0 | |
| Seq. id. mode 0 | |
| Alternative alignments 0 | |
| Coverage threshold 0 | |
| Coverage mode 0 | |
| Max sequence length 65535 | |
| 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 | |
| Seed substitution matrix nucl:nucleotide.out,aa:VTML80.out | |
| Sensitivity 4 | |
| 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 30 | |
| 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 true | |
| Report mode 0 | |
| Alignment format 0 | |
| Format alignment output query,target,fident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits | |
| Database output false | |
| First sequence as representative false | |
| Target column 1 | |
| Add full header false | |
| Sequence source 0 | |
| Database type 0 | |
| Shuffle input database true | |
| Createdb mode 1 | |
| Write lookup file 0 | |
| createdb e77760e07c3167ef94f937365175d68b.assm.combined.fasta /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/query --dbtype 0 --shuffle 1 --createdb-mode 1 --write-lookup 0 --id-offset 0 --compressed 0 -v 3 | |
| Shuffle database cannot be combined with --createdb-mode 0 | |
| We recompute with --shuffle 0 | |
| Converting sequences | |
| [Multiline fasta can not be combined with --createdb-mode 0 | |
| We recompute with --createdb-mode 1 | |
| Time for merging to query_h: 0h 0m 0s 0ms | |
| Time for merging to query: 0h 0m 0s 0ms | |
| [ | |
| Time for merging to query_h: 0h 0m 0s 0ms | |
| Time for merging to query: 0h 0m 0s 0ms | |
| Database type: Nucleotide | |
| Time for processing: 0h 0m 0s 12ms | |
| Create directory /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp | |
| taxonomy /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/query DB/uniref50-tax/UniRef50 /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/result /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp --orf-filter 1 --lca-mode 3 --tax-output-mode 2 --majority 0.5 --vote-mode 1 --lca-ranks superkingdom,phylum,class,order,family,genus --tax-lineage 2 --threads 32 --remove-tmp-files 1 | |
| extractorfs /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/query /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_aa --min-length 30 --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 1 --use-all-table-starts 0 --id-offset 0 --create-lookup 0 --threads 32 --compressed 0 -v 3 | |
| [=================================================================] 2 0s 33ms | |
| Time for merging to orfs_aa_h: 0h 0m 0s 1ms | |
| Time for merging to orfs_aa: 0h 0m 0s 1ms | |
| Time for processing: 0h 0m 0s 139ms | |
| prefilter /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_aa DB/uniref50-tax/UniRef50 /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_pref --sub-mat nucl:nucleotide.out,aa:blosum62.out --seed-sub-mat nucl:nucleotide.out,aa:VTML80.out -s 2 -k 0 --k-score 2147483647 --alph-size nucl:5,aa:21 --max-seq-len 65535 --max-seqs 1 --split 0 --split-mode 2 --split-memory-limit 0 -c 0 --cov-mode 0 --comp-bias-corr 1 --diag-score 0 --exact-kmer-matching 0 --mask 1 --mask-lower-case 0 --min-ungapped-score 3 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 0 --pca 1 --pcb 1.5 --threads 32 --compressed 0 -v 3 | |
| Query database size: 15 type: Aminoacid | |
| Estimated memory consumption: 151G | |
| Target database size: 43032414 type: Aminoacid | |
| Index table k-mer threshold: 163 at k-mer size 7 | |
| Index table: counting k-mers | |
| [=================================================================] 43.03M 4m 2s 212ms | |
| Index table: Masked residues: 327874438 | |
| Index table: fill | |
| [=================================================================] 43.03M 11m 49s 219ms | |
| Index statistics | |
| Entries: 10015666182 | |
| DB size: 67075 MB | |
| Avg k-mer size: 7.824739 | |
| Top 10 k-mers | |
| DFEQLPH 65289 | |
| NVPGWSP 65148 | |
| FRYAFPS 64963 | |
| RYYVLGW 64817 | |
| VDRLNTQ 63812 | |
| WRLDFLN 62949 | |
| TVDGDFS 62609 | |
| NKTDFVQ 61859 | |
| QDWVQIP 61316 | |
| LDGAYVP 59471 | |
| Time for index table init: 0h 16m 24s 811ms | |
| Process prefiltering step 1 of 1 | |
| k-mer similarity threshold: 163 | |
| Starting prefiltering scores calculation (step 1 of 1) | |
| Query db start 1 to 15 | |
| Target db start 1 to 43032414 | |
| [=================================================================] 15 0s 59ms | |
| 0.355339 k-mers per position | |
| 274 DB matches per sequence | |
| 0 overflows | |
| 0 queries produce too many hits (truncated result) | |
| 0 sequences passed prefiltering per query sequence | |
| 0 median result list length | |
| 15 sequences with 0 size result lists | |
| Time for merging to orfs_pref: 0h 0m 0s 2ms | |
| Time for processing: 0h 16m 45s 727ms | |
| rescorediagonal /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_aa DB/uniref50-tax/UniRef50 /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_pref /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_aln --sub-mat nucl:nucleotide.out,aa:blosum62.out --rescore-mode 2 --wrapped-scoring 0 --filter-hits 0 -e 100 -c 0 -a 0 --cov-mode 0 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --add-self-matches 0 --sort-results 0 --db-load-mode 0 --threads 32 --compressed 0 -v 3 | |
| [=================================================================] 15 0s 21ms | |
| Time for merging to orfs_aln: 0h 0m 0s 2ms | |
| Time for processing: 0h 0m 19s 666ms | |
| createsubdb /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_aln.list /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_aa /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_filter --subdb-mode 1 -v 3 | |
| Time for merging to orfs_filter: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 1ms | |
| rmdb /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_filter_h -v 3 | |
| Time for processing: 0h 0m 0s 0ms | |
| createsubdb /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_aln.list /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_aa_h /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_filter_h --subdb-mode 1 -v 3 | |
| Time for merging to orfs_filter_h: 0h 0m 0s 0ms | |
| Time for processing: 0h 0m 0s 1ms | |
| Create directory /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/tmp_taxonomy | |
| taxonomy /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_filter DB/uniref50-tax/UniRef50 /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_tax /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/tmp_taxonomy --orf-filter 1 --lca-mode 3 --tax-output-mode 2 --majority 0.5 --vote-mode 1 --lca-ranks superkingdom,phylum,class,order,family,genus --tax-lineage 0 --threads 32 --alignment-mode 1 -e 1 --max-rejected 5 --max-accept 30 -s 2 --spaced-kmer-mode 1 --min-length 30 --max-length 32734 --orf-start-mode 1 --remove-tmp-files 1 | |
| Create directory /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/tmp_taxonomy/4936078414881223269/tmp_hsp1 | |
| search /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_filter DB/uniref50-tax/UniRef50 /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/tmp_taxonomy/4936078414881223269/first /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/tmp_taxonomy/4936078414881223269/tmp_hsp1 --alignment-mode 1 -e 1 --max-rejected 5 --max-accept 30 --threads 32 -s 2 --spaced-kmer-mode 1 --min-length 30 --max-length 32734 --orf-start-mode 1 --lca-search 1 --remove-tmp-files 1 | |
| prefilter /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_filter DB/uniref50-tax/UniRef50 /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/tmp_taxonomy/4936078414881223269/tmp_hsp1/16551820070899017371/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 65535 --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 32 --compressed 0 -v 3 -s 2.0 | |
| Query database size: 0 type: Aminoacid | |
| Estimated memory consumption: 151G | |
| Target database size: 43032414 type: Aminoacid | |
| Index table k-mer threshold: 163 at k-mer size 7 | |
| Index table: counting k-mers | |
| [=================================================================] 43.03M 4m 11s 993ms | |
| Index table: Masked residues: 327874438 | |
| Index table: fill | |
| [=================================================================] 43.03M 11m 31s 69ms | |
| Index statistics | |
| Entries: 10015666182 | |
| DB size: 67075 MB | |
| Avg k-mer size: 7.824739 | |
| Top 10 k-mers | |
| DFEQLPH 65289 | |
| NVPGWSP 65148 | |
| FRYAFPS 64963 | |
| RYYVLGW 64817 | |
| VDRLNTQ 63812 | |
| WRLDFLN 62949 | |
| TVDGDFS 62609 | |
| NKTDFVQ 61859 | |
| QDWVQIP 61316 | |
| LDGAYVP 59471 | |
| Time for index table init: 0h 16m 9s 488ms | |
| Time for processing: 0h 16m 22s 538ms | |
| lcaalign /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/orfs_filter DB/uniref50-tax/UniRef50 /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/tmp_taxonomy/4936078414881223269/tmp_hsp1/16551820070899017371/pref_0 /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/tmp_taxonomy/4936078414881223269/first --sub-mat nucl:nucleotide.out,aa:blosum62.out -a 0 --alignment-mode 1 --alignment-output-mode 0 --wrapped-scoring 0 -e 1 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 65535 --comp-bias-corr 1 --max-rejected 5 --max-accept 30 --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 32 --compressed 0 -v 3 | |
| Input /dev/shm/tmp/contig-taxonomy/e77760e07c3167ef94f937365175d68b.tax.UniRef50/12595762918832005520/taxonomy_tmp/13584421311535647719/tmp_taxonomy/4936078414881223269/tmp_hsp1/16551820070899017371/pref_0 does not exist | |
| Error: Alignment died | |
| Error: First search died | |
| Error: taxonomy died | |
| Error: Search died |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment