# 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_bacteria.hmm # target sequence database: - # output directed to file: ssu/ssu.bacteria.txt # hits tabular output: ssu/ssu.bacteria.table.txt # show alignments in output: no # sequence reporting threshold: E-value <= 1e-05 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: bacteria [M=1523] Scores for complete hits: E-value score bias Sequence start end Description ------- ------ ----- -------- ----- ----- ----------- 0 1353.8 25.9 NZ_CP019035.1 465535 467086 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 0 1353.8 25.9 NZ_CP019035.1 508865 510416 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 0 1353.8 25.9 NZ_CP019035.1 668122 669673 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 0 1353.8 25.9 NZ_CP019035.1 762659 764210 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 0 1353.8 25.9 NZ_CP019035.1 1449183 1450734 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 0 1353.8 25.9 NZ_CP019035.1 3853959 3852408 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 0 1353.8 25.9 NZ_CP019035.1 4559197 4557646 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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 1353.8 25.9 0 27 1514 .. 465535 467086 .. 465514 467096 .. 4609911 0.95 >> 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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 1353.8 25.9 0 27 1514 .. 508865 510416 .. 508844 510426 .. 4609911 0.95 >> 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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 1353.8 25.9 0 27 1514 .. 668122 669673 .. 668101 669683 .. 4609911 0.95 >> 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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 1353.8 25.9 0 27 1514 .. 762659 764210 .. 762638 764220 .. 4609911 0.95 >> 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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 1353.8 25.9 0 27 1514 .. 1449183 1450734 .. 1449162 1450744 .. 4609911 0.95 >> 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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 1353.8 25.9 0 27 1514 .. 3853959 3852408 .. 3853980 3852398 .. 4609911 0.95 >> 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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 1353.8 25.9 0 27 1514 .. 4559197 4557646 .. 4559218 4557636 .. 4609911 0.95 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1523 nodes) Target sequences: 1 (9219822 residues searched) Residues passing SSV filter: 229910 (0.0249); expected (0.02) Residues passing bias filter: 221212 (0.024); expected (0.02) Residues passing Vit filter: 26778 (0.0029); expected (0.003) Residues passing Fwd filter: 15911 (0.00173); expected (3e-05) Total number of hits: 7 (0.00118) # CPU time: 2.48u 0.20s 00:00:02.68 Elapsed: 00:00:00.47 # Mc/sec: 29876.15 // [ok]