Mercurial > repos > iuc > hmmer_hmmalign

annotate test-data/MADE1.nhmmscan_out @ 4:ca0b674e895b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
author iuc
date Mon, 11 Jun 2018 15:51:03 -0400
parents a9c62fc8187b
children b2453ee52845
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a9c62fc8187b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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1 # nhmmscan :: search DNA sequence(s) against a DNA profile database
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ca0b674e895b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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2 # HMMER 3.2 (June 2018); http://hmmer.org/
ca0b674e895b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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3 # Copyright (C) 2018 Howard Hughes Medical Institute.
ca0b674e895b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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4 # Freely distributed under the BSD open source license.
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5 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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ca0b674e895b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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6 # query sequence file: /tmp/tmpp4O0Ju/files/000/dataset_41.dat
ca0b674e895b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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7 # target HMM database: localref.hmm
ca0b674e895b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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8 # per-seq hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_43.dat
ca0b674e895b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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9 # hits output in Dfam format: /tmp/tmpp4O0Ju/files/000/dataset_44.dat
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a9c62fc8187b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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10 # max ASCII text line length: unlimited
a9c62fc8187b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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11 # Vit filter P threshold: <= 0.001
a9c62fc8187b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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12 # Fwd filter P threshold: <= 1e-05
a9c62fc8187b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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13 # random number seed set to: 4
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14 # number of worker threads: 1
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15 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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a9c62fc8187b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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17 Query: humanchr1/239220001-239550000 [L=330000]
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18 Scores for complete hit:
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19 E-value score bias Model start end Description
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20 ------- ------ ----- -------- ----- ----- -----------
4
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21 8.7e-11 39.2 7.4 MADE1 302390 302466 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
ca0b674e895b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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22 6.4e-08 30.0 8.3 MADE1 174456 174498 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
ca0b674e895b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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23 9.3e-08 29.5 6.1 MADE1 302466 302390 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
ca0b674e895b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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24 6.3e-06 23.7 7.0 MADE1 174493 174456 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
3
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25 ------ inclusion threshold ------
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26 1.4 6.5 7.0 MADE1 304073 304104 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
3
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29 Annotation for each hit (and alignments):
a9c62fc8187b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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30 >> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
a9c62fc8187b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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31 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to mod len acc
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32 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----
4
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33 ! 39.2 7.4 8.7e-11 4 80 .] 302390 302466 .. 302387 302466 .. 80 0.87
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35 Alignment:
4
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36 score: 39.2 bits
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37 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
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38 MADE1 4 ggttggtgcaaaagtaattgcggtttttgccattacttttaatggc....aaaaaccgcaattacttttgcaccaacctaa 80
4
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39 ggt ggtgcaaaa aattg ggtttttgccatt cttttaat gc a aaa g a t ctttt caccaa ctaa
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40 humanchr1/239220001-239550000 302390 GGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCttttA-AAA--GT-AATGCTTTTACACCAATCTAA 302466
ca0b674e895b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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41 899******************************************955533.443..33.44689************9986 PP
3
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43 >> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
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44 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to mod len acc
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45 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----
4
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46 ! 30.0 8.3 6.4e-08 1 43 [. 174456 174498 .. 174456 174518 .. 80 0.92
3
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48 Alignment:
4
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49 score: 30.0 bits
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50 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
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51 MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt 43
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52 ttaggtt gtgcaaaagtaattg ggtttttg cattactttt
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53 humanchr1/239220001-239550000 174456 TTAGGTTAGTGCAAAAGTAATTGTGGTTTTTGTCATTACTTTT 174498
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54 589************************************9975 PP
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56 >> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
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57 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to mod len acc
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58 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----
4
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59 ! 29.5 6.1 9.3e-08 1 77 [. 302466 302390 .. 302466 302387 .. 80 0.74
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61 Alignment:
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62 score: 29.5 bits
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63 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
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64 MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt................aatggcaaaaaccgcaattacttttgcaccaacc 77
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65 ttag ttggtg aaaag cattactttt aatggcaaaaacc caatt ttttgcacc acc
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66 humanchr1/239220001-239550000 302466 TTAGATTGGTGTAAAAG----------------CATTACTTTTaaaagcaattaaaagcAATGGCAAAAACCACAATTGATTTTGCACCGACC 302390
4
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67 68999999999999998................4666777765222222222222222268****************************9998 PP
3
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69 >> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
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70 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to mod len acc
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71 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----
4
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72 ! 23.7 7.0 6.3e-06 43 80 .] 174493 174456 .. 174513 174456 .. 80 0.91
3
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74 Alignment:
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75 score: 23.7 bits
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76 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
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77 MADE1 43 taatggcaaaaaccgcaattacttttgcaccaacctaa 80
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78 taatg caaaaacc caattacttttgcac aacctaa
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79 humanchr1/239220001-239550000 174493 TAATGACAAAAACCACAATTACTTTTGCACTAACCTAA 174456
4
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80 689********************************986 PP
3
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81
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82 >> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
a9c62fc8187b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit fa7dec5f222510d58f566f4799a04e3731fa03f6
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83 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to mod len acc
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84 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----
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85 ? 6.5 7.0 1.4 41 72 .. 304073 304104 .. 304053 304109 .. 80 0.85
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86
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87 Alignment:
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88 score: 6.5 bits
3
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89 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
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90 MADE1 41 tttaatggcaaaaaccgcaattacttttgcac 72
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91 tt a tgg aaaaa ca tta ttttgca
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92 humanchr1/239220001-239550000 304073 TTAAGTGGGAAAAAATACACTTATTTTTGCAT 304104
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93 455779************************86 PP
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94
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95
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96
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97 Internal pipeline statistics summary:
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98 -------------------------------------
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99 Query sequence(s): 1 (660000 residues searched)
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100 Target model(s): 1 (80 nodes)
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101 Residues passing SSV filter: 63737 (0.0966); expected (0.02)
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102 Residues passing bias filter: 44695 (0.0677); expected (0.02)
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103 Residues passing Vit filter: 2309 (0.0035); expected (0.001)
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104 Residues passing Fwd filter: 2041 (0.00309); expected (1e-05)
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105 Total number of hits: 5 (0.000405)
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106 # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
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107 # Mc/sec: 2407.09
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108 //
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109 [ok]