Mercurial > repos > iuc > hmmer3

annotate test-data/MADE1.out @ 1:b5066aa77fea draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit f7d83adb11624763b9b113f938a1d5f311c8f9fa-dirty
author iuc
date Sat, 19 Sep 2015 17:05:45 -0400
parents 62479bdcc059
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62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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1 # hmmscan :: search sequence(s) against a profile database
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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2 # HMMER 3.1b1 (May 2013); http://hmmer.org/
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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3 # Copyright (C) 2013 Howard Hughes Medical Institute.
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4 # Freely distributed under the GNU General Public License (GPLv3).
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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5 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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6 # query sequence file: test-data/dna_target.fa
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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7 # target HMM database: test-data/MADE1.hmm
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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8 # per-seq hits tabular output: t.tbl
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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9 # per-dom hits tabular output: t.domtbl
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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10 # pfam-style tabular hit output: t.pfamtbl
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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11 # max ASCII text line length: unlimited
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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12 # Vit filter P threshold: <= 0.001
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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13 # Fwd filter P threshold: <= 1e-05
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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14 # random number seed set to: 4
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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15 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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16
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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17 Query: humanchr1/239220001-239550000 [L=330000]
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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18 Scores for complete sequence (score includes all domains):
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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19 --- full sequence --- --- best 1 domain --- -#dom-
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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20 E-value score bias E-value score bias exp N Model Description
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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21 ------- ------ ----- ------- ------ ----- ---- -- -------- -----------
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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22 7.1e-18 51.5 28.5 2e-12 34.0 0.7 9.6 5 MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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23
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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24
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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25 Domain annotation for each model (and alignments):
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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26 >> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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27 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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28 --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
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29 1 ? -4.3 0.1 1 1 30 54 .. 80044 80068 .. 80030 80073 .. 0.80
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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30 2 ? -6.7 3.3 1 1 13 71 .. 154012 154072 .. 154011 154076 .. 0.75
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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31 3 ! 27.6 0.7 2e-10 2e-10 1 44 [. 174456 174514 .. 174456 174577 .. 0.62
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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32 4 ! 34.0 0.7 2e-12 2e-12 2 80 .] 302388 302466 .. 302387 302466 .. 0.86
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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33 5 ? 2.8 0.7 0.011 0.011 27 75 .. 304060 304107 .. 304021 304109 .. 0.61
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34
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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35 Alignments for each domain:
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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36 == domain 1 score: -4.3 bits; conditional E-value: 1
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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37 xxxxxxxxxxxxxxxxxxxxxxxxx RF
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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38 MADE1 30 ttgccattacttttaatggcaaaaa 54
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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39 t g catt ttt aatggcaaa a
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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40 humanchr1/239220001-239550000 80044 TAGTCATTCATTTCAATGGCAAATA 80068
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41 45789****************9966 PP
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42
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43 == domain 2 score: -6.7 bits; conditional E-value: 1
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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44 xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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45 MADE1 13 aaaagtaattgcggtttttgccatt......acttttaatggcaaaaaccgcaattacttttgca 71
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46 aaaagta tt + ttttgc att a tttaa gcaaa a + tta tttgca
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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47 humanchr1/239220001-239550000 154012 AAAAGTAGTTTTCAATTTTGCAATTtgaccaATATTTAAATGCAAATATT----TTATATTTGCA 154072
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48 78999999999999999999999984444444457777777899998876....77777888876 PP
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49
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50 == domain 3 score: 27.6 bits; conditional E-value: 2e-10
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51 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...............x RF
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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52 MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt...............a 44
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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53 ttaggtt gtgcaaaagtaattg+ggtttttg cattactttt a
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54 humanchr1/239220001-239550000 174456 TTAGGTTAGTGCAAAAGTAATTGTGGTTTTTGTCATTACTTTTctgcatgctagaagtA 174514
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55 79***************************************964443333333333330 PP
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56
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57 == domain 4 score: 34.0 bits; conditional E-value: 2e-12
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58 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
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59 MADE1 2 taggttggtgcaaaagtaattgcggtttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaacctaa 80
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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60 t ggt ggtgcaaaa aattg+ggtttttgccatt cttttaat gc a + a t ctttt caccaa ctaa
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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61 humanchr1/239220001-239550000 302388 TTGGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCTTTTAAAAGTAATGCTTTTACACCAATCTAA 302466
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62 56899******************************************963333233345578**************997 PP
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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63
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64 == domain 5 score: 2.8 bits; conditional E-value: 0.011
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65 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
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66 MADE1 27 tttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaa 75
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
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67 tttt g c ta tt a tgg aaaaa ++ca tta ttttgca aa
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68 humanchr1/239220001-239550000 304060 TTTTAGACTATA-GTTAAGTGGGAAAAAATACACTTATTTTTGCATTAA 304107
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69 222222222222.3455779************************98765 PP
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70
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71
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72
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73 Internal pipeline statistics summary:
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74 -------------------------------------
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75 Query sequence(s): 1 (330000 residues searched)
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76 Target model(s): 1 (80 nodes)
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77 Passed MSV filter: 1 (1); expected 0.0 (0.02)
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78 Passed bias filter: 1 (1); expected 0.0 (0.02)
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79 Passed Vit filter: 1 (1); expected 0.0 (0.001)
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80 Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
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81 Initial search space (Z): 1 [actual number of targets]
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82 Domain search space (domZ): 1 [number of targets reported over threshold]
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83 # CPU time: 0.52u 0.03s 00:00:00.55 Elapsed: 00:00:00.54
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84 # Mc/sec: 48.89
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
85 //
62479bdcc059 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4164b44c651bcbdac6637eccce61b2a802c9b569
iuc
parents:
diff changeset
86 [ok]