Mercurial > repos > iuc > hmmer_nhmmscan

annotate test-data/nhmmer.out @ 1:4351ee79c942 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 2c4b4a154e2f07730fdfdaf66a09e1e09ac5efde
author iuc
date Mon, 14 Nov 2016 15:12:05 -0500
parents a6098dd0cb46
children f68b43be32d7
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a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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1 # nhmmer :: search a DNA model or alignment against a DNA database
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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2 # HMMER 3.1b2 (February 2015); http://hmmer.org/
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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3 # Copyright (C) 2015 Howard Hughes Medical Institute.
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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4 # Freely distributed under the GNU General Public License (GPLv3).
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5 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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6 # query file: /tmp/tmpprnvgs/files/000/dataset_1.dat
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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7 # target sequence database: /tmp/tmpprnvgs/files/000/dataset_2.dat
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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8 # hits tabular output: /tmp/tmpprnvgs/files/000/dataset_4.dat
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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9 # hits output in Dfam format: None
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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10 # max ASCII text line length: unlimited
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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11 # SSV filter P threshold: <= 0.02
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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12 # Vit filter P threshold: <= 0.001
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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13 # Fwd filter P threshold: <= 1e-05
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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14 # input query is asserted as: DNA
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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15 # random number seed set to: 4
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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16 # number of worker threads: 1
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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17 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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18
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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19 Query: MADE1 [M=80]
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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20 Accession: DF0000629.2
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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21 Description: MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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22 Scores for complete hits:
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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23 E-value score bias Sequence start end Description
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24 ------- ------ ----- -------- ----- ----- -----------
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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25 1.2e-10 38.6 7.4 humanchr1/239220001-239550000 302390 302466
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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26 7.8e-08 29.6 8.3 humanchr1/239220001-239550000 174456 174498
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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27 1.2e-07 28.9 6.0 humanchr1/239220001-239550000 302466 302390
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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28 7.2e-06 23.3 7.0 humanchr1/239220001-239550000 174493 174456
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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29 ------ inclusion threshold ------
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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30 1.4 6.3 7.0 humanchr1/239220001-239550000 304073 304104
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31
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32
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33 Annotation for each hit (and alignments):
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34 >> humanchr1/239220001-239550000
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35 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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36 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----
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37 ! 38.6 7.4 1.2e-10 4 80 .] 302390 302466 .. 302387 302466 .. 330000 0.87
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38
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39 Alignment:
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40 score: 38.6 bits
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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41 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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42 MADE1 4 ggttggtgcaaaagtaattgcggtttttgccattacttttaatggc....aaaaaccgcaattacttttgcaccaacctaa 80
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43 ggt ggtgcaaaa aattg ggtttttgccatt cttttaat gc a aaa g a t ctttt caccaa ctaa
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44 humanchr1/239220001-239550000 302390 GGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCttttA-AAA--GTA-ATGCTTTTACACCAATCTAA 302466
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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45 899******************************************955533.443..334.4689***********99986 PP
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46
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47 >> humanchr1/239220001-239550000
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48 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc
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49 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----
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50 ! 29.6 8.3 7.8e-08 1 43 [. 174456 174498 .. 174456 174518 .. 330000 0.92
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51
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52 Alignment:
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53 score: 29.6 bits
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54 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
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55 MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt 43
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56 ttaggtt gtgcaaaagtaattg ggtttttg cattactttt
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57 humanchr1/239220001-239550000 174456 TTAGGTTAGTGCAAAAGTAATTGTGGTTTTTGTCATTACTTTT 174498
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58 589************************************9975 PP
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59
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60 >> humanchr1/239220001-239550000
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61 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc
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62 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----
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63 ! 28.9 6.0 1.2e-07 1 77 [. 302466 302390 .. 302466 302387 .. 330000 0.74
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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64
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65 Alignment:
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66 score: 28.9 bits
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67 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
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68 MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt................aatggcaaaaaccgcaattacttttgcaccaacc 77
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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69 ttag ttggtg aaaag cattactttt aatggcaaaaacc caatt ttttgcacc acc
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70 humanchr1/239220001-239550000 302466 TTAGATTGGTGTAAAAG----------------CATTACTTTTaaaagcaattaaaagcAATGGCAAAAACCACAATTGATTTTGCACCGACC 302390
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71 68999999999999998................5666777776222222222222222268****************************9998 PP
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72
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73 >> humanchr1/239220001-239550000
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74 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc
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75 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----
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76 ! 23.3 7.0 7.2e-06 43 80 .] 174493 174456 .. 174513 174456 .. 330000 0.91
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77
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78 Alignment:
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79 score: 23.3 bits
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80 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
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81 MADE1 43 taatggcaaaaaccgcaattacttttgcaccaacctaa 80
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82 taatg caaaaacc caattacttttgcac aacctaa
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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83 humanchr1/239220001-239550000 174493 TAATGACAAAAACCACAATTACTTTTGCACTAACCTAA 174456
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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84 689********************************985 PP
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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85
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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86 >> humanchr1/239220001-239550000
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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87 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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88 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----
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89 ? 6.3 7.0 1.4 41 72 .. 304073 304104 .. 304053 304109 .. 330000 0.85
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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90
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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91 Alignment:
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92 score: 6.3 bits
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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93 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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94 MADE1 41 tttaatggcaaaaaccgcaattacttttgcac 72
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95 tt a tgg aaaaa ca tta ttttgca
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96 humanchr1/239220001-239550000 304073 TTAAGTGGGAAAAAATACACTTATTTTTGCAT 304104
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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97 455779************************86 PP
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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98
a6098dd0cb46 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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99
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100
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101 Internal pipeline statistics summary:
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102 -------------------------------------
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103 Query model(s): 1 (80 nodes)
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104 Target sequences: 1 (660000 residues searched)
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105 Residues passing SSV filter: 61794 (0.0936); expected (0.02)
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106 Residues passing bias filter: 46199 (0.07); expected (0.02)
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107 Residues passing Vit filter: 2752 (0.00417); expected (0.001)
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108 Residues passing Fwd filter: 2526 (0.00383); expected (1e-05)
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109 Total number of hits: 5 (0.000405)
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110 # CPU time: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.03
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111 # Mc/sec: 1760.00
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112 //
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113 [ok]