Mercurial > repos > iuc > hmmer_phmmer

annotate test-data/MADE1.out @ 4:74fc6d7d40f1 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 15:50:40 -0400
parents 48a88b7a4734
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48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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1 # hmmscan :: search sequence(s) against a profile database
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2 # HMMER 3.2 (June 2018); http://hmmer.org/
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3 # Copyright (C) 2018 Howard Hughes Medical Institute.
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4 # Freely distributed under the BSD open source license.
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5 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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6 # query sequence file: /tmp/tmpp4O0Ju/files/000/dataset_20.dat
74fc6d7d40f1 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
74fc6d7d40f1 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_22.dat
74fc6d7d40f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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9 # per-dom hits tabular output: /tmp/tmpp4O0Ju/files/000/dataset_23.dat
74fc6d7d40f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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10 # pfam-style tabular hit output: /tmp/tmpp4O0Ju/files/000/dataset_24.dat
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48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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11 # max ASCII text line length: unlimited
48a88b7a4734 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
48a88b7a4734 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
48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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14 # random number seed set to: 4
48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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15 # number of worker threads: 1
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16 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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18 Query: humanchr1/239220001-239550000 [L=330000]
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19 Scores for complete sequence (score includes all domains):
48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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20 --- full sequence --- --- best 1 domain --- -#dom-
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21 E-value score bias E-value score bias exp N Model Description
48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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22 ------- ------ ----- ------- ------ ----- ---- -- -------- -----------
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23 5.7e-18 51.8 27.9 2e-12 34.1 0.7 9.6 5 MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
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48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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26 Domain annotation for each model (and alignments):
48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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27 >> MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
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28 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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29 --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
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30 1 ? -4.5 0.0 1 1 30 54 .. 80044 80068 .. 80033 80072 .. 0.81
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31 2 ? -6.6 3.3 1 1 13 71 .. 154012 154072 .. 154011 154076 .. 0.75
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32 3 ! 27.4 0.7 2.4e-10 2.4e-10 1 43 [. 174456 174498 .. 174456 174577 .. 0.66
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33 4 ! 34.1 0.7 2e-12 2e-12 2 80 .] 302388 302466 .. 302387 302466 .. 0.86
74fc6d7d40f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
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34 5 ? 2.8 0.7 0.011 0.011 27 75 .. 304060 304107 .. 304022 304109 .. 0.62
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36 Alignments for each domain:
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37 == domain 1 score: -4.5 bits; conditional E-value: 1
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38 xxxxxxxxxxxxxxxxxxxxxxxxx RF
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39 MADE1 30 ttgccattacttttaatggcaaaaa 54
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40 t g catt ttt aatggcaaa a
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41 humanchr1/239220001-239550000 80044 TAGTCATTCATTTCAATGGCAAATA 80068
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42 457899***************9865 PP
0
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43
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44 == domain 2 score: -6.6 bits; conditional E-value: 1
48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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45 xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
4
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46 MADE1 13 aaaagtaattgcggtttttgccatt......acttttaatggcaaaaaccgcaattacttttgca 71
0
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47 aaaagta tt + ttttgc att a tttaa gcaaa a + tta tttgca
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48 humanchr1/239220001-239550000 154012 AAAAGTAGTTTTCAATTTTGCAATTtgaccaATATTTAAATGCAAATATT----TTATATTTGCA 154072
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49 78999999999999999999999984444444457777777899988765....67777778776 PP
0
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50
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51 == domain 3 score: 27.4 bits; conditional E-value: 2.4e-10
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52 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
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53 MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt 43
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54 ttaggtt gtgcaaaagtaattg+ggtttttg cattactttt
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55 humanchr1/239220001-239550000 174456 TTAGGTTAGTGCAAAAGTAATTGTGGTTTTTGTCATTACTTTT 174498
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56 79**************************************996 PP
0
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57
4
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58 == domain 4 score: 34.1 bits; conditional E-value: 2e-12
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59 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
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60 MADE1 2 taggttggtgcaaaagtaattgcggtttttgccattacttttaatggca...aaaaccgcaattacttttgcaccaacctaa 80
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61 t ggt ggtgcaaaa aattg+ggtttttgccatt cttttaat gc aaaa g a t ctttt caccaa ctaa
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62 humanchr1/239220001-239550000 302388 TTGGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCTtttAAAA--G-TAATGCTTTTACACCAATCTAA 302466
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63 56899******************************************962223333..3.45578**************997 PP
0
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64
4
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65 == domain 5 score: 2.8 bits; conditional E-value: 0.011
0
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66 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
4
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67 MADE1 27 tttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaa 75
0
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68 tttt g c ta tt a tgg aaaaa ++ca tta ttttgca aa
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69 humanchr1/239220001-239550000 304060 TTTTAGACTATA-GTTAAGTGGGAAAAAATACACTTATTTTTGCATTAA 304107
4
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70 222223222222.3556779************************98765 PP
0
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74 Internal pipeline statistics summary:
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75 -------------------------------------
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76 Query sequence(s): 1 (330000 residues searched)
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77 Target model(s): 1 (80 nodes)
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78 Passed MSV filter: 1 (1); expected 0.0 (0.02)
48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
79 Passed bias filter: 1 (1); expected 0.0 (0.02)
48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
80 Passed Vit filter: 1 (1); expected 0.0 (0.001)
48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
81 Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
82 Initial search space (Z): 1 [actual number of targets]
48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
83 Domain search space (domZ): 1 [number of targets reported over threshold]
4
74fc6d7d40f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
iuc
parents: 0
diff changeset
84 # CPU time: 0.14u 0.01s 00:00:00.15 Elapsed: 00:00:00.14
74fc6d7d40f1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7c3ac4ad5a64b737e1b8f73c522e006097596f1d
iuc
parents: 0
diff changeset
85 # Mc/sec: 177.58
0
48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
86 //
48a88b7a4734 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
87 [ok]