# cmscan :: search sequence(s) against a CM database # INFERNAL 1.1.4 (Dec 2020) # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query sequence file: 23S00176-1.fna # target CM database: /mnt/data/db/bakta/db/rRNA # CM configuration: glocal # show alignments in output: no # model-specific thresholding: TC cutoffs # Rfam pipeline mode: on [strict filtering] # HMM-only mode for 0 basepair models: no # number of worker threads: 24 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: 1 [L=1905426] Hit scores: rank E-value score bias modelname start end mdl trunc gc description ---- --------- ------ ----- ----------------- ------- ------- --- ----- ---- ----------- (1) ! 1.4e-48 1569.8 12.5 SSU_rRNA_bacteria 163634 165172 + cm no 0.51 Bacterial small subunit ribosomal RNA (2) ! 1.4e-48 1569.8 12.5 SSU_rRNA_bacteria 169066 170604 + cm no 0.51 Bacterial small subunit ribosomal RNA (3) ! 1.4e-48 1569.8 12.5 SSU_rRNA_bacteria 525263 526801 + cm no 0.51 Bacterial small subunit ribosomal RNA (4) ! 1.4e-48 1569.8 12.5 SSU_rRNA_bacteria 1211698 1210160 - cm no 0.51 Bacterial small subunit ribosomal RNA (5) ! 1.4e-48 1569.8 12.5 SSU_rRNA_bacteria 1217130 1215592 - cm no 0.51 Bacterial small subunit ribosomal RNA (6) ! 1.4e-48 1569.8 12.5 SSU_rRNA_bacteria 1222562 1221024 - cm no 0.51 Bacterial small subunit ribosomal RNA (7) ! 2.8e-09 63.4 0.0 5S_rRNA 168455 168568 + cm no 0.48 5S ribosomal RNA (8) ! 2.8e-09 63.4 0.0 5S_rRNA 173887 174000 + cm no 0.48 5S ribosomal RNA (9) ! 2.8e-09 63.4 0.0 5S_rRNA 530084 530197 + cm no 0.48 5S ribosomal RNA (10) ! 2.8e-09 63.4 0.0 5S_rRNA 1206877 1206764 - cm no 0.48 5S ribosomal RNA (11) ! 2.8e-09 63.4 0.0 5S_rRNA 1212309 1212196 - cm no 0.48 5S ribosomal RNA (12) ! 2.8e-09 63.4 0.0 5S_rRNA 1217741 1217628 - cm no 0.48 5S ribosomal RNA (13) ! 3.8e-05 2869.0 49.4 LSU_rRNA_bacteria 165481 168378 + cm no 0.50 Bacterial large subunit ribosomal RNA (14) ! 3.8e-05 2869.0 49.4 LSU_rRNA_bacteria 170913 173810 + cm no 0.50 Bacterial large subunit ribosomal RNA (15) ! 3.8e-05 2869.0 49.4 LSU_rRNA_bacteria 527110 530007 + cm no 0.50 Bacterial large subunit ribosomal RNA (16) ! 3.8e-05 2869.0 49.4 LSU_rRNA_bacteria 1209851 1206954 - cm no 0.50 Bacterial large subunit ribosomal RNA (17) ! 3.8e-05 2869.0 49.4 LSU_rRNA_bacteria 1215283 1212386 - cm no 0.50 Bacterial large subunit ribosomal RNA (18) ! 3.8e-05 2869.0 49.4 LSU_rRNA_bacteria 1220715 1217818 - cm no 0.50 Bacterial large subunit ribosomal RNA Internal CM pipeline statistics summary: ---------------------------------------- Query sequence(s): 1 (3810852 residues searched) Query sequences re-searched for truncated hits: 1 (7934.7 residues re-searched, avg per model) Target model(s): 3 (4577 consensus positions) Windows passing local HMM SSV filter: 747 (0.07015); expected (0.06) Windows passing local HMM Viterbi filter: 128 (0.008847); expected (0.02) Windows passing local HMM Viterbi bias filter: 124 (0.007845); expected (0.02) Windows passing local HMM Forward filter: 18 (0.004372); expected (0.0002) Windows passing local HMM Forward bias filter: 18 (0.004372); expected (0.0002) Windows passing glocal HMM Forward filter: 15 (0.004372); expected (0.0002) Windows passing glocal HMM Forward bias filter: 15 (0.004372); expected (0.0002) Envelopes passing glocal HMM envelope defn filter: 18 (0.002394); expected (0.0002) Envelopes passing glocal CM CYK filter: 18 (0.002393); expected (0.0001) Total CM hits reported: 18 (0.002383); includes 0 truncated hit(s) # CPU time: 26.15u 2.81s 00:00:28.95 Elapsed: 00:00:23.35 // Query: 2 [L=9362] Hit scores: rank E-value score bias modelname start end mdl trunc gc description ---- --------- ------ ----- --------- ------ ------ --- ----- ---- ----------- [No hits detected that satisfy reporting thresholds] Internal CM pipeline statistics summary: ---------------------------------------- Query sequence(s): 1 (18724 residues searched) Query sequences re-searched for truncated hits: 1 (7934.7 residues re-searched, avg per model) Target model(s): 3 (4577 consensus positions) Windows passing local HMM SSV filter: 2 (0.1146); expected (0.06) Windows passing local HMM Viterbi filter: 0 (0); expected (0.02) Windows passing local HMM Viterbi bias filter: 0 (0); expected (0.02) Windows passing local HMM Forward filter: 0 (0); expected (0.0002) Windows passing local HMM Forward bias filter: 0 (0); expected (0.0002) Windows passing glocal HMM Forward filter: 0 (0); expected (0.0002) Windows passing glocal HMM Forward bias filter: 0 (0); expected (0.0002) Envelopes passing glocal HMM envelope defn filter: 0 (0); expected (0.0002) Envelopes passing glocal CM CYK filter: 0 (0); expected (0.0001) Total CM hits reported: 0 (0); includes 0 truncated hit(s) # CPU time: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.06 // [ok]