Mercurial > repos > iuc > hmmer_jackhmmer
comparison test-data/nhmmer.out @ 5:5113c71c7031 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
author | iuc |
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date | Tue, 16 Jun 2020 05:32:33 -0400 |
parents | 793967b6ae8a |
children | 6e27bb3f0fa6 |
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4:793967b6ae8a | 5:5113c71c7031 |
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1 # nhmmer :: search a DNA model, alignment, or sequence against a DNA database | 1 # nhmmer :: search a DNA model, alignment, or sequence against a DNA database |
2 # HMMER 3.2 (June 2018); http://hmmer.org/ | 2 # HMMER 3.3 (Nov 2019); http://hmmer.org/ |
3 # Copyright (C) 2018 Howard Hughes Medical Institute. | 3 # Copyright (C) 2019 Howard Hughes Medical Institute. |
4 # Freely distributed under the BSD open source license. | 4 # Freely distributed under the BSD open source license. |
5 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | 5 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
6 # query file: /tmp/tmpp4O0Ju/files/000/dataset_36.dat | 6 # query file: /tmp/tmpqydies2m/files/c/4/e/dataset_c4e67f40-cb86-438e-8bc0-6020ada9fc86.dat |
7 # target sequence database: /tmp/tmpp4O0Ju/files/000/dataset_37.dat | 7 # target sequence database: /tmp/tmpqydies2m/files/a/1/b/dataset_a1b4364c-0e9a-4709-b4ef-ab7e5661d9e9.dat |
8 # hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_39.dat | 8 # hits tabular output: /tmp/tmpqydies2m/files/b/d/d/dataset_bdd87d82-1ce1-4051-8d5f-f7251bf7fd18.dat |
9 # hits output in Dfam format: None | 9 # hits output in Dfam format: /tmp/tmpqydies2m/files/d/8/e/dataset_d8ee0d50-d171-4e8a-9c7d-1cbd4394296f.dat |
10 # alignment scores output: /tmp/tmpqydies2m/files/5/1/3/dataset_5139892f-c507-40c4-b43d-f73023c634f4.dat | |
10 # max ASCII text line length: unlimited | 11 # max ASCII text line length: unlimited |
11 # SSV filter P threshold: <= 0.02 | 12 # SSV filter P threshold: <= 0.02 |
12 # Vit filter P threshold: <= 0.001 | 13 # Vit filter P threshold: <= 0.001 |
13 # Fwd filter P threshold: <= 1e-05 | 14 # Fwd filter P threshold: <= 1e-05 |
14 # input query is asserted as: DNA | 15 # input query is asserted as: DNA |
20 Accession: DF0000629.2 | 21 Accession: DF0000629.2 |
21 Description: MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon | 22 Description: MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon |
22 Scores for complete hits: | 23 Scores for complete hits: |
23 E-value score bias Sequence start end Description | 24 E-value score bias Sequence start end Description |
24 ------- ------ ----- -------- ----- ----- ----------- | 25 ------- ------ ----- -------- ----- ----- ----------- |
25 8.7e-11 39.2 7.4 humanchr1/239220001-239550000 302390 302466 | 26 4e-11 41.3 7.5 humanchr1/239220001-239550000 302390 302466 |
26 6.4e-08 30.0 8.3 humanchr1/239220001-239550000 174456 174498 | 27 1.9e-08 32.8 8.3 humanchr1/239220001-239550000 174456 174498 |
27 9.3e-08 29.5 6.1 humanchr1/239220001-239550000 302466 302390 | 28 6.3e-08 31.0 6.7 humanchr1/239220001-239550000 302466 302389 |
28 6.3e-06 23.7 7.0 humanchr1/239220001-239550000 174493 174456 | 29 4.9e-06 25.0 7.0 humanchr1/239220001-239550000 174493 174456 |
29 ------ inclusion threshold ------ | 30 ------ inclusion threshold ------ |
30 1.4 6.5 7.0 humanchr1/239220001-239550000 304073 304104 | 31 2.2 6.9 7.2 humanchr1/239220001-239550000 304073 304103 |
31 | 32 |
32 | 33 |
33 Annotation for each hit (and alignments): | 34 Annotation for each hit (and alignments): |
34 >> humanchr1/239220001-239550000 | 35 >> humanchr1/239220001-239550000 |
35 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc | 36 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc |
36 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- | 37 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- |
37 ! 39.2 7.4 8.7e-11 4 80 .] 302390 302466 .. 302387 302466 .. 330000 0.87 | 38 ! 41.3 7.5 4e-11 4 80 .] 302390 302466 .. 302387 302466 .. 330000 0.88 |
38 | 39 |
39 Alignment: | 40 Alignment: |
40 score: 39.2 bits | 41 score: 41.3 bits |
41 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF | 42 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF |
42 MADE1 4 ggttggtgcaaaagtaattgcggtttttgccattacttttaatggc....aaaaaccgcaattacttttgcaccaacctaa 80 | 43 MADE1 4 ggttggtgcaaaagtaattgcggtttttgccattacttttaatggc....aaaaaccgcaattacttttgcaccaacctaa 80 |
43 ggt ggtgcaaaa aattg ggtttttgccatt cttttaat gc a aaa g a t ctttt caccaa ctaa | 44 ggt ggtgcaaaa aattg ggtttttgccatt cttttaat gc aaaa g a t ctttt caccaa ctaa |
44 humanchr1/239220001-239550000 302390 GGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCttttA-AAA--GT-AATGCTTTTACACCAATCTAA 302466 | 45 humanchr1/239220001-239550000 302390 GGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCttttAAAA---GT-AATGCTTTTACACCAATCTAA 302466 |
45 899******************************************955533.443..33.44689************9986 PP | 46 89*******************************************966644554...34.4578**************997 PP |
46 | 47 |
47 >> humanchr1/239220001-239550000 | 48 >> humanchr1/239220001-239550000 |
48 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc | 49 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc |
49 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- | 50 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- |
50 ! 30.0 8.3 6.4e-08 1 43 [. 174456 174498 .. 174456 174518 .. 330000 0.92 | 51 ! 32.8 8.3 1.9e-08 1 43 [. 174456 174498 .. 174456 174518 .. 330000 0.91 |
51 | 52 |
52 Alignment: | 53 Alignment: |
53 score: 30.0 bits | 54 score: 32.8 bits |
54 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF | 55 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF |
55 MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt 43 | 56 MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt 43 |
56 ttaggtt gtgcaaaagtaattg ggtttttg cattactttt | 57 ttaggtt gtgcaaaagtaattg ggtttttg cattactttt |
57 humanchr1/239220001-239550000 174456 TTAGGTTAGTGCAAAAGTAATTGTGGTTTTTGTCATTACTTTT 174498 | 58 humanchr1/239220001-239550000 174456 TTAGGTTAGTGCAAAAGTAATTGTGGTTTTTGTCATTACTTTT 174498 |
58 589************************************9975 PP | 59 589************************************9986 PP |
59 | 60 |
60 >> humanchr1/239220001-239550000 | 61 >> humanchr1/239220001-239550000 |
61 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc | 62 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc |
62 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- | 63 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- |
63 ! 29.5 6.1 9.3e-08 1 77 [. 302466 302390 .. 302466 302387 .. 330000 0.74 | 64 ! 31.0 6.7 6.3e-08 1 78 [. 302466 302389 .. 302466 302387 .. 330000 0.80 |
64 | 65 |
65 Alignment: | 66 Alignment: |
66 score: 29.5 bits | 67 score: 31.0 bits |
67 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF | 68 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF |
68 MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt................aatggcaaaaaccgcaattacttttgcaccaacc 77 | 69 MADE1 1 ttaggttggtgcaaaagtaattgcggttttt....gccattacttttaatggcaaaaaccgcaattacttttgcaccaacct 78 |
69 ttag ttggtg aaaag cattactttt aatggcaaaaacc caatt ttttgcacc acc | 70 ttag ttggtg aaaag a t tttt gc atta +aatggcaaaaacc caatt ttttgcacc acc |
70 humanchr1/239220001-239550000 302466 TTAGATTGGTGTAAAAG----------------CATTACTTTTaaaagcaattaaaagcAATGGCAAAAACCACAATTGATTTTGCACCGACC 302390 | 71 humanchr1/239220001-239550000 302466 TTAGATTGGTGTAAAAGCATT-A---CTTTTaaaaGCAATTAAAAGCAATGGCAAAAACCACAATTGATTTTGCACCGACCA 302389 |
71 68999999999999998................4666777765222222222222222268****************************9998 PP | 72 6899************97543.2...23333455566666666666799*****************************9985 PP |
72 | 73 |
73 >> humanchr1/239220001-239550000 | 74 >> humanchr1/239220001-239550000 |
74 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc | 75 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc |
75 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- | 76 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- |
76 ! 23.7 7.0 6.3e-06 43 80 .] 174493 174456 .. 174513 174456 .. 330000 0.91 | 77 ! 25.0 7.0 4.9e-06 43 80 .] 174493 174456 .. 174513 174456 .. 330000 0.94 |
77 | 78 |
78 Alignment: | 79 Alignment: |
79 score: 23.7 bits | 80 score: 25.0 bits |
80 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF | 81 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF |
81 MADE1 43 taatggcaaaaaccgcaattacttttgcaccaacctaa 80 | 82 MADE1 43 taatggcaaaaaccgcaattacttttgcaccaacctaa 80 |
82 taatg caaaaacc caattacttttgcac aacctaa | 83 taatg caaaaacc caattacttttgcac aacctaa |
83 humanchr1/239220001-239550000 174493 TAATGACAAAAACCACAATTACTTTTGCACTAACCTAA 174456 | 84 humanchr1/239220001-239550000 174493 TAATGACAAAAACCACAATTACTTTTGCACTAACCTAA 174456 |
84 689********************************986 PP | 85 5899*******************************986 PP |
85 | 86 |
86 >> humanchr1/239220001-239550000 | 87 >> humanchr1/239220001-239550000 |
87 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc | 88 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc |
88 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- | 89 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ---- |
89 ? 6.5 7.0 1.4 41 72 .. 304073 304104 .. 304053 304109 .. 330000 0.85 | 90 ? 6.9 7.2 2.2 41 71 .. 304073 304103 .. 304053 304109 .. 330000 0.85 |
90 | 91 |
91 Alignment: | 92 Alignment: |
92 score: 6.5 bits | 93 score: 6.9 bits |
93 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF | 94 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF |
94 MADE1 41 tttaatggcaaaaaccgcaattacttttgcac 72 | 95 MADE1 41 tttaatggcaaaaaccgcaattacttttgca 71 |
95 tt a tgg aaaaa ca tta ttttgca | 96 tt a tgg aaaaa ca tta ttttgca |
96 humanchr1/239220001-239550000 304073 TTAAGTGGGAAAAAATACACTTATTTTTGCAT 304104 | 97 humanchr1/239220001-239550000 304073 TTAAGTGGGAAAAAATACACTTATTTTTGCA 304103 |
97 455779************************86 PP | 98 456789************************8 PP |
98 | 99 |
99 | 100 |
100 | 101 |
101 Internal pipeline statistics summary: | 102 Internal pipeline statistics summary: |
102 ------------------------------------- | 103 ------------------------------------- |
103 Query model(s): 1 (80 nodes) | 104 Query model(s): 1 (80 nodes) |
104 Target sequences: 1 (660000 residues searched) | 105 Target sequences: 1 (660000 residues searched) |
105 Residues passing SSV filter: 63737 (0.0966); expected (0.02) | 106 Residues passing SSV filter: 60770 (0.0921); expected (0.02) |
106 Residues passing bias filter: 44695 (0.0677); expected (0.02) | 107 Residues passing bias filter: 35792 (0.0542); expected (0.02) |
107 Residues passing Vit filter: 2309 (0.0035); expected (0.001) | 108 Residues passing Vit filter: 1612 (0.00244); expected (0.001) |
108 Residues passing Fwd filter: 2041 (0.00309); expected (1e-05) | 109 Residues passing Fwd filter: 1194 (0.00181); expected (1e-05) |
109 Total number of hits: 5 (0.000405) | 110 Total number of hits: 5 (0.000405) |
110 # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02 | 111 # CPU time: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.05 |
111 # Mc/sec: 1854.66 | 112 # Mc/sec: 1031.54 |
112 // | 113 // |
113 [ok] | 114 [ok] |