# nhmmer :: search a DNA model or alignment against a DNA database # HMMER 3.1b2 (February 2015); http://hmmer.org/ # Copyright (C) 2015 Howard Hughes Medical Institute. # Freely distributed under the GNU General Public License (GPLv3). # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query file: /usr/local/src/CheckM-1.0.7/data/hmms_ssu/SSU_euk.hmm # target sequence database: - # output directed to file: ssu/ssu.euk.txt # hits tabular output: ssu/ssu.euk.table.txt # show alignments in output: no # sequence reporting threshold: E-value <= 1e-05 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: silva.eukarya [M=1734] Scores for complete hits: E-value score bias Sequence start end Description ------- ------ ----- -------- ----- ----- ----------- 4e-82 272.9 12.8 NZ_CP019035.1 466207 466962 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 4e-82 272.9 12.8 NZ_CP019035.1 509537 510292 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 4e-82 272.9 12.8 NZ_CP019035.1 668794 669549 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 4e-82 272.9 12.8 NZ_CP019035.1 763331 764086 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 4e-82 272.9 12.8 NZ_CP019035.1 1449855 1450610 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 4e-82 272.9 12.8 NZ_CP019035.1 3853287 3852532 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 4e-82 272.9 12.8 NZ_CP019035.1 4558525 4557770 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 Annotation for each hit : >> NZ_CP019035.1 Salmonella enterica subsp. enterica serovar Gallinarum str. 9184, complete genome score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 272.9 12.8 4e-82 857 1638 .. 466207 466962 .. 466187 466989 .. 4609911 0.82 >> NZ_CP019035.1 Salmonella enterica subsp. enterica serovar Gallinarum str. 9184, complete genome score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 272.9 12.8 4e-82 857 1638 .. 509537 510292 .. 509517 510319 .. 4609911 0.82 >> NZ_CP019035.1 Salmonella enterica subsp. enterica serovar Gallinarum str. 9184, complete genome score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 272.9 12.8 4e-82 857 1638 .. 668794 669549 .. 668774 669576 .. 4609911 0.82 >> NZ_CP019035.1 Salmonella enterica subsp. enterica serovar Gallinarum str. 9184, complete genome score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 272.9 12.8 4e-82 857 1638 .. 763331 764086 .. 763311 764113 .. 4609911 0.82 >> NZ_CP019035.1 Salmonella enterica subsp. enterica serovar Gallinarum str. 9184, complete genome score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 272.9 12.8 4e-82 857 1638 .. 1449855 1450610 .. 1449835 1450637 .. 4609911 0.82 >> NZ_CP019035.1 Salmonella enterica subsp. enterica serovar Gallinarum str. 9184, complete genome score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 272.9 12.8 4e-82 857 1638 .. 3853287 3852532 .. 3853307 3852505 .. 4609911 0.82 >> NZ_CP019035.1 Salmonella enterica subsp. enterica serovar Gallinarum str. 9184, complete genome score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 272.9 12.8 4e-82 857 1638 .. 4558525 4557770 .. 4558545 4557743 .. 4609911 0.82 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1734 nodes) Target sequences: 1 (9219822 residues searched) Residues passing SSV filter: 275838 (0.0299); expected (0.02) Residues passing bias filter: 275838 (0.0299); expected (0.02) Residues passing Vit filter: 122128 (0.0132); expected (0.003) Residues passing Fwd filter: 88718 (0.00962); expected (3e-05) Total number of hits: 7 (0.000574) # CPU time: 4.00u 0.18s 00:00:04.18 Elapsed: 00:00:00.78 # Mc/sec: 20496.37 // [ok]