# 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_archaea.hmm # target sequence database: - # output directed to file: ssu/ssu.archaea.txt # hits tabular output: ssu/ssu.archaea.table.txt # show alignments in output: no # sequence reporting threshold: E-value <= 1e-05 # number of worker threads: 8 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: archaea [M=1381] Scores for complete hits: E-value score bias Sequence start end Description ------- ------ ----- -------- ----- ----- ----------- 2.3e-202 673.3 26.4 NZ_CP019035.1 465583 467080 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 2.3e-202 673.3 26.4 NZ_CP019035.1 508913 510410 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 2.3e-202 673.3 26.4 NZ_CP019035.1 668170 669667 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 2.3e-202 673.3 26.4 NZ_CP019035.1 762707 764204 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 2.3e-202 673.3 26.4 NZ_CP019035.1 1449231 1450728 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 2.3e-202 673.3 26.4 NZ_CP019035.1 3853911 3852414 Salmonella enterica subsp. enterica serovar Gallinarum str. 9 2.3e-202 673.3 26.4 NZ_CP019035.1 4559149 4557652 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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 673.3 26.4 2.3e-202 41 1378 .. 465583 467080 .. 465555 467083 .. 4609911 0.91 >> 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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 673.3 26.4 2.3e-202 41 1378 .. 508913 510410 .. 508885 510413 .. 4609911 0.91 >> 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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 673.3 26.4 2.3e-202 41 1378 .. 668170 669667 .. 668142 669670 .. 4609911 0.91 >> 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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 673.3 26.4 2.3e-202 41 1378 .. 762707 764204 .. 762679 764207 .. 4609911 0.91 >> 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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 673.3 26.4 2.3e-202 41 1378 .. 1449231 1450728 .. 1449203 1450731 .. 4609911 0.91 >> 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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 673.3 26.4 2.3e-202 41 1378 .. 3853911 3852414 .. 3853939 3852411 .. 4609911 0.91 >> 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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- ! 673.3 26.4 2.3e-202 41 1378 .. 4559149 4557652 .. 4559177 4557649 .. 4609911 0.91 Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (1381 nodes) Target sequences: 1 (9219822 residues searched) Residues passing SSV filter: 334906 (0.0363); expected (0.02) Residues passing bias filter: 315321 (0.0342); expected (0.02) Residues passing Vit filter: 40931 (0.00444); expected (0.003) Residues passing Fwd filter: 19189 (0.00208); expected (3e-05) Total number of hits: 7 (0.00114) # CPU time: 2.34u 0.18s 00:00:02.52 Elapsed: 00:00:00.44 # Mc/sec: 28937.67 // [ok]