Mercurial > repos > iuc > hmmer_hmmemit

annotate test-data/nhmmer.out @ 4:1cd4d0cf8fd9 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 15:51:54 -0400
parents f48f9bbfcfd8
children 9415f29a3926
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4
1cd4d0cf8fd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
iuc
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1 # nhmmer :: search a DNA model, alignment, or sequence against a DNA database
1cd4d0cf8fd9 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/
1cd4d0cf8fd9 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.
1cd4d0cf8fd9 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.
0
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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5 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
4
1cd4d0cf8fd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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6 # query file: /tmp/tmpp4O0Ju/files/000/dataset_36.dat
1cd4d0cf8fd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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7 # target sequence database: /tmp/tmpp4O0Ju/files/000/dataset_37.dat
1cd4d0cf8fd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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8 # hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_39.dat
0
f48f9bbfcfd8 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
f48f9bbfcfd8 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
f48f9bbfcfd8 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
f48f9bbfcfd8 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
f48f9bbfcfd8 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
f48f9bbfcfd8 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
f48f9bbfcfd8 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
f48f9bbfcfd8 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
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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17 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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18
f48f9bbfcfd8 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]
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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20 Accession: DF0000629.2
f48f9bbfcfd8 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
f48f9bbfcfd8 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:
f48f9bbfcfd8 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
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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24 ------- ------ ----- -------- ----- ----- -----------
4
1cd4d0cf8fd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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25 8.7e-11 39.2 7.4 humanchr1/239220001-239550000 302390 302466
1cd4d0cf8fd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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26 6.4e-08 30.0 8.3 humanchr1/239220001-239550000 174456 174498
1cd4d0cf8fd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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27 9.3e-08 29.5 6.1 humanchr1/239220001-239550000 302466 302390
1cd4d0cf8fd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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28 6.3e-06 23.7 7.0 humanchr1/239220001-239550000 174493 174456
0
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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29 ------ inclusion threshold ------
4
1cd4d0cf8fd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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30 1.4 6.5 7.0 humanchr1/239220001-239550000 304073 304104
0
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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33 Annotation for each hit (and alignments):
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34 >> humanchr1/239220001-239550000
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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35 score bias Evalue hmmfrom hmm to alifrom ali to envfrom env to sq len acc
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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36 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----
4
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37 ! 39.2 7.4 8.7e-11 4 80 .] 302390 302466 .. 302387 302466 .. 330000 0.87
0
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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38
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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39 Alignment:
4
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40 score: 39.2 bits
0
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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41 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
f48f9bbfcfd8 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
4
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43 ggt ggtgcaaaa aattg ggtttttgccatt cttttaat gc a aaa g a t ctttt caccaa ctaa
1cd4d0cf8fd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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44 humanchr1/239220001-239550000 302390 GGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCttttA-AAA--GT-AATGCTTTTACACCAATCTAA 302466
1cd4d0cf8fd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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45 899******************************************955533.443..33.44689************9986 PP
0
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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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----
4
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50 ! 30.0 8.3 6.4e-08 1 43 [. 174456 174498 .. 174456 174518 .. 330000 0.92
0
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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51
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52 Alignment:
4
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53 score: 30.0 bits
0
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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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----
4
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63 ! 29.5 6.1 9.3e-08 1 77 [. 302466 302390 .. 302466 302387 .. 330000 0.74
0
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64
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65 Alignment:
4
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66 score: 29.5 bits
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67 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
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68 MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt................aatggcaaaaaccgcaattacttttgcaccaacc 77
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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
4
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71 68999999999999998................4666777765222222222222222268****************************9998 PP
0
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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 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----
4
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76 ! 23.7 7.0 6.3e-06 43 80 .] 174493 174456 .. 174513 174456 .. 330000 0.91
0
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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77
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78 Alignment:
4
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79 score: 23.7 bits
0
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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80 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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81 MADE1 43 taatggcaaaaaccgcaattacttttgcaccaacctaa 80
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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82 taatg caaaaacc caattacttttgcac aacctaa
f48f9bbfcfd8 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
4
1cd4d0cf8fd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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84 689********************************986 PP
0
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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85
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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86 >> humanchr1/239220001-239550000
f48f9bbfcfd8 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
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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88 ------ ----- --------- ------- ------- --------- --------- --------- --------- --------- ----
4
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89 ? 6.5 7.0 1.4 41 72 .. 304073 304104 .. 304053 304109 .. 330000 0.85
0
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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90
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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91 Alignment:
4
1cd4d0cf8fd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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92 score: 6.5 bits
0
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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93 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
f48f9bbfcfd8 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
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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95 tt a tgg aaaaa ca tta ttttgca
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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96 humanchr1/239220001-239550000 304073 TTAAGTGGGAAAAAATACACTTATTTTTGCAT 304104
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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97 455779************************86 PP
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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98
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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99
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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100
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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101 Internal pipeline statistics summary:
f48f9bbfcfd8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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102 -------------------------------------
4
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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: 63737 (0.0966); expected (0.02)
1cd4d0cf8fd9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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106 Residues passing bias filter: 44695 (0.0677); expected (0.02)
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107 Residues passing Vit filter: 2309 (0.0035); expected (0.001)
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108 Residues passing Fwd filter: 2041 (0.00309); expected (1e-05)
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109 Total number of hits: 5 (0.000405)
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110 # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
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111 # Mc/sec: 1854.66
0
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112 //
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113 [ok]