Mercurial > repos > iuc > hmmer_hmmsearch

annotate test-data/MADE1.out @ 5:b774ae8e1609 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
author iuc
date Tue, 16 Jun 2020 05:27:07 -0400
parents 6867ed975e25
children d753d9169482
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1dde27bbdcba 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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b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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2 # HMMER 3.3 (Nov 2019); http://hmmer.org/
b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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3 # Copyright (C) 2019 Howard Hughes Medical Institute.
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4 # Freely distributed under the BSD open source license.
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1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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5 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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6 # query sequence file: /tmp/tmpqydies2m/files/5/d/3/dataset_5d34ccc7-9920-470e-9f13-678ab2ecd29d.dat
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7 # target HMM database: localref.hmm
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8 # per-seq hits tabular output: /tmp/tmpqydies2m/files/1/d/a/dataset_1da10e33-3e1c-48fc-abfb-7e3c263ec0df.dat
b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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9 # per-dom hits tabular output: /tmp/tmpqydies2m/files/7/2/3/dataset_723f3cf1-e0de-4616-aec7-dd16680f3be3.dat
b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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10 # pfam-style tabular hit output: /tmp/tmpqydies2m/files/7/3/4/dataset_734c7f25-0a22-431b-9a7a-58849fcd6009.dat
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1dde27bbdcba 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
1dde27bbdcba 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
1dde27bbdcba 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
1dde27bbdcba 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
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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):
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20 --- full sequence --- --- best 1 domain --- -#dom-
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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21 E-value score bias E-value score bias exp N Model Description
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22 ------- ------ ----- ------- ------ ----- ---- -- -------- -----------
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23 9.3e-18 51.2 26.3 1.3e-12 34.8 0.7 8.6 4 MADE1 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
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26 Domain annotation for each model (and alignments):
1dde27bbdcba 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
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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28 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
1dde27bbdcba 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 ! 27.4 0.6 2.4e-10 2.4e-10 1 43 [. 174456 174498 .. 174456 174520 .. 0.93
b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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31 2 ? -8.4 5.8 1 1 12 79 .. 197274 197341 .. 197272 197342 .. 0.86
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32 3 ! 34.8 0.7 1.3e-12 1.3e-12 2 80 .] 302388 302466 .. 302387 302466 .. 0.87
b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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33 4 ? 1.4 0.4 0.033 0.033 27 74 .. 304060 304106 .. 304029 304108 .. 0.71
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1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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35 Alignments for each domain:
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36 == domain 1 score: 27.4 bits; conditional E-value: 2.4e-10
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37 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
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38 MADE1 1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt 43
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39 ttaggtt gtgcaaaagtaattg+ggtttttg cattactttt
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40 humanchr1/239220001-239550000 174456 TTAGGTTAGTGCAAAAGTAATTGTGGTTTTTGTCATTACTTTT 174498
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41 79**************************************997 PP
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42
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43 == domain 2 score: -8.4 bits; conditional E-value: 1
b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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44 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
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45 MADE1 12 caaaagtaattgcggtttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaaccta 79
b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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46 caa gtaatt + tttt c att ttt t c aaa c c tta tt t ac a cta
b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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47 humanchr1/239220001-239550000 197274 CAATGGTAATTTTATTTTTAACTATTTTATTTTTTAACTAAACTCACTTTTATTTATTTACATATCTA 197341
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48 567789*******************999999999999*****99999999999988877777776666 PP
0
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49
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50 == domain 3 score: 34.8 bits; conditional E-value: 1.3e-12
b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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51 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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52 MADE1 2 taggttggtgcaaaagtaattgcggtttttgccattacttttaatggcaaaaaccgcaattacttttgcaccaacctaa 80
b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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53 t ggt ggtgcaaaa aattg+ggtttttgccatt cttttaat gc a a t ctttt caccaa ctaa
b774ae8e1609 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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54 humanchr1/239220001-239550000 302388 TTGGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCTTTTAAAAGTAATGCTTTTACACCAATCTAA 302466
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55 6799*****************************************99953333333345578**************997 PP
0
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56
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57 == domain 4 score: 1.4 bits; conditional E-value: 0.033
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58 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
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59 MADE1 27 tttttgccattacttttaatggcaaaaaccgcaattacttttgcacca 74
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60 tttt g c ta tt a tgg aaaaa + ca tta ttttgca a
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61 humanchr1/239220001-239550000 304060 TTTTAGACTATA-GTTAAGTGGGAAAAAATACACTTATTTTTGCATTA 304106
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62 334444443333.356788*************************9766 PP
0
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64
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66 Internal pipeline statistics summary:
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67 -------------------------------------
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68 Query sequence(s): 1 (330000 residues searched)
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69 Target model(s): 1 (80 nodes)
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70 Passed MSV filter: 1 (1); expected 0.0 (0.02)
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71 Passed bias filter: 1 (1); expected 0.0 (0.02)
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72 Passed Vit filter: 1 (1); expected 0.0 (0.001)
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73 Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
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74 Initial search space (Z): 1 [actual number of targets]
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75 Domain search space (domZ): 1 [number of targets reported over threshold]
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76 # CPU time: 0.21u 0.01s 00:00:00.22 Elapsed: 00:00:00.22
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77 # Mc/sec: 117.29
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1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
78 //
1dde27bbdcba planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
iuc
parents:
diff changeset
79 [ok]