Mercurial > repos > iuc > hmmer_hmmfetch
diff test-data/phmmer.out @ 7:a28fd001de59 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 0bccf5220ed6549db7e053f85bbe917326b0a0be"
| author | iuc |
|---|---|
| date | Wed, 21 Jul 2021 14:14:16 +0000 |
| parents | 74089c182a50 |
| children |
line wrap: on
line diff
--- a/test-data/phmmer.out Thu Jan 14 15:42:21 2021 +0000 +++ b/test-data/phmmer.out Wed Jul 21 14:14:16 2021 +0000 @@ -1,18 +1,15 @@ # phmmer :: search a protein sequence against a protein database -# HMMER 3.2 (June 2018); http://hmmer.org/ -# Copyright (C) 2018 Howard Hughes Medical Institute. +# HMMER 3.3.2 (Nov 2020); http://hmmer.org/ +# Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -# query sequence file: /tmp/tmpp4O0Ju/files/000/dataset_45.dat -# target sequence database: /tmp/tmpp4O0Ju/files/000/dataset_46.dat -# per-seq hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_48.dat -# per-dom hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_49.dat -# pfam-style tabular hit output: /tmp/tmpp4O0Ju/files/000/dataset_50.dat +# query sequence file: /tmp/tmpzdnl83p_/files/f/3/7/dataset_f37673ce-2825-4214-827f-9fd8798aa730.dat +# target sequence database: /tmp/tmpzdnl83p_/files/4/8/e/dataset_48ee2b1d-0f10-4a66-bc8d-a3f4938d2e4a.dat # max ASCII text line length: unlimited # Vit filter P threshold: <= 0.001 # Fwd filter P threshold: <= 1e-05 # random number seed set to: 4 -# number of worker threads: 1 +# number of worker threads: 0 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: MYG_ESCGI [L=153] @@ -62,7 +59,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 2.67 +# Mc/sec: 2.88 // Query: MYG_HORSE [L=153] Scores for complete sequences (score includes all domains): @@ -111,7 +108,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.81 +# Mc/sec: 3.02 // Query: MYG_PROGU [L=153] Scores for complete sequences (score includes all domains): @@ -159,8 +156,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.81 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 3.01 // Query: MYG_SAISC [L=153] Scores for complete sequences (score includes all domains): @@ -208,8 +205,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 2.78 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 3.04 // Query: MYG_LYCPI [L=153] Scores for complete sequences (score includes all domains): @@ -257,8 +254,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.74 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 3.06 // Query: MYG_MOUSE [L=153] Scores for complete sequences (score includes all domains): @@ -306,8 +303,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 2.78 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 3.08 // Query: MYG_MUSAN [L=148] Scores for complete sequences (score includes all domains): @@ -355,8 +352,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.88 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 3.08 // Query: HBA_AILME [L=141] Scores for complete sequences (score includes all domains): @@ -404,8 +401,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 2.80 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 3.00 // Query: HBA_PROLO [L=141] Scores for complete sequences (score includes all domains): @@ -453,8 +450,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.73 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 3.00 // Query: HBA_PAGLA [L=141] Scores for complete sequences (score includes all domains): @@ -503,7 +500,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.33 +# Mc/sec: 3.03 // Query: HBA_MACFA [L=141] Scores for complete sequences (score includes all domains): @@ -552,7 +549,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 2.65 +# Mc/sec: 3.00 // Query: HBA_MACSI [L=141] Scores for complete sequences (score includes all domains): @@ -600,8 +597,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.73 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 3.03 // Query: HBA_PONPY [L=141] Scores for complete sequences (score includes all domains): @@ -650,7 +647,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.67 +# Mc/sec: 2.97 // Query: HBA2_GALCR [L=141] Scores for complete sequences (score includes all domains): @@ -699,7 +696,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 2.68 +# Mc/sec: 3.01 // Query: HBA_MESAU [L=141] Scores for complete sequences (score includes all domains): @@ -748,7 +745,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.41 +# Mc/sec: 3.00 // Query: HBA2_BOSMU [L=141] Scores for complete sequences (score includes all domains): @@ -796,8 +793,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.64 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 3.02 // Query: HBA_ERIEU [L=141] Scores for complete sequences (score includes all domains): @@ -846,7 +843,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 2.76 +# Mc/sec: 2.92 // Query: HBA_FRAPO [L=141] Scores for complete sequences (score includes all domains): @@ -895,7 +892,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.70 +# Mc/sec: 2.60 // Query: HBA_PHACO [L=141] Scores for complete sequences (score includes all domains): @@ -944,7 +941,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 2.56 +# Mc/sec: 2.51 // Query: HBA_TRIOC [L=141] Scores for complete sequences (score includes all domains): @@ -993,7 +990,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.35 +# Mc/sec: 2.58 // Query: HBA_ANSSE [L=141] Scores for complete sequences (score includes all domains): @@ -1041,8 +1038,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 2.52 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 2.51 // Query: HBA_COLLI [L=141] Scores for complete sequences (score includes all domains): @@ -1091,7 +1088,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.79 +# Mc/sec: 2.44 // Query: HBAD_CHLME [L=141] Scores for complete sequences (score includes all domains): @@ -1139,8 +1136,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 1.87 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 2.83 // Query: HBAD_PASMO [L=141] Scores for complete sequences (score includes all domains): @@ -1188,8 +1185,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 2.10 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 2.91 // Query: HBAZ_HORSE [L=141] Scores for complete sequences (score includes all domains): @@ -1238,7 +1235,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.21 +# Mc/sec: 2.95 // Query: HBA4_SALIR [L=142] Scores for complete sequences (score includes all domains): @@ -1287,7 +1284,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 2.72 +# Mc/sec: 2.98 // Query: HBB_ORNAN [L=146] Scores for complete sequences (score includes all domains): @@ -1336,7 +1333,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.63 +# Mc/sec: 2.92 // Query: HBB_TACAC [L=146] Scores for complete sequences (score includes all domains): @@ -1384,8 +1381,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.82 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 3.01 // Query: HBE_PONPY [L=146] Scores for complete sequences (score includes all domains): @@ -1433,8 +1430,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.02 -# Mc/sec: 1.68 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 3.03 // Query: HBB_SPECI [L=146] Scores for complete sequences (score includes all domains): @@ -1482,8 +1479,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 2.16 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 2.97 // Query: HBB_SPETO [L=146] Scores for complete sequences (score includes all domains): @@ -1532,7 +1529,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.50 +# Mc/sec: 2.97 // Query: HBB_EQUHE [L=146] Scores for complete sequences (score includes all domains): @@ -1580,8 +1577,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 2.16 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 2.98 // Query: HBB_SUNMU [L=146] Scores for complete sequences (score includes all domains): @@ -1629,8 +1626,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 2.00 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 2.91 // Query: HBB_CALAR [L=146] Scores for complete sequences (score includes all domains): @@ -1678,8 +1675,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02 -# Mc/sec: 1.87 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 2.78 // Query: HBB_MANSP [L=146] Scores for complete sequences (score includes all domains): @@ -1727,8 +1724,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 1.86 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 2.75 // Query: HBB_URSMA [L=146] Scores for complete sequences (score includes all domains): @@ -1776,8 +1773,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 1.65 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 2.74 // Query: HBB_RABIT [L=146] Scores for complete sequences (score includes all domains): @@ -1825,8 +1822,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.57 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 2.56 // Query: HBB_TUPGL [L=146] Scores for complete sequences (score includes all domains): @@ -1875,7 +1872,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.80 +# Mc/sec: 2.49 // Query: HBB_TRIIN [L=146] Scores for complete sequences (score includes all domains): @@ -1923,8 +1920,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 -# Mc/sec: 2.80 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 2.55 // Query: HBB_COLLI [L=146] Scores for complete sequences (score includes all domains): @@ -1973,7 +1970,7 @@ Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 -# Mc/sec: 2.22 +# Mc/sec: 2.43 // Query: HBB_LARRI [L=146] Scores for complete sequences (score includes all domains): @@ -2021,8 +2018,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 1.82 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 2.45 // Query: HBB1_VAREX [L=146] Scores for complete sequences (score includes all domains): @@ -2070,8 +2067,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 1.75 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 2.70 // Query: HBB2_XENTR [L=146] Scores for complete sequences (score includes all domains): @@ -2119,8 +2116,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02 -# Mc/sec: 1.82 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 2.72 // Query: HBBL_RANCA [L=146] Scores for complete sequences (score includes all domains): @@ -2168,8 +2165,8 @@ Passed Fwd filter: 2 (1); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 2 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 1.80 +# CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 +# Mc/sec: 2.69 // Query: HBB2_TRICR [L=145] Scores for complete sequences (score includes all domains): @@ -2204,7 +2201,7 @@ Passed Fwd filter: 1 (0.5); expected 0.0 (1e-05) Initial search space (Z): 2 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] -# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 -# Mc/sec: 1.87 +# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 +# Mc/sec: 2.57 // [ok]