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comparison test-data/meme_output_txt_1.txt @ 0:fd522a964017 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260
author iuc
date Tue, 22 Dec 2015 17:01:51 -0500
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1 ********************************************************************************
2 MEME - Motif discovery tool
3 ********************************************************************************
4 MEME version 4.11.0 (Release date: Thu Nov 26 17:48:49 2015 +1000)
5
6 For further information on how to interpret these results or to get
7 a copy of the MEME software please access http://meme-suite.org .
8
9 This file may be used as input to the MAST algorithm for searching
10 sequence databases for matches to groups of motifs. MAST is available
11 for interactive use and downloading at http://meme-suite.org .
12 ********************************************************************************
13
14
15 ********************************************************************************
16 REFERENCE
17 ********************************************************************************
18 If you use this program in your research, please cite:
19
20 Timothy L. Bailey and Charles Elkan,
21 "Fitting a mixture model by expectation maximization to discover
22 motifs in biopolymers", Proceedings of the Second International
23 Conference on Intelligent Systems for Molecular Biology, pp. 28-36,
24 AAAI Press, Menlo Park, California, 1994.
25 ********************************************************************************
26
27
28 ********************************************************************************
29 TRAINING SET
30 ********************************************************************************
31 DATAFILE= /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat
32 ALPHABET= ACDEFGHIKLMNPQRSTVWY
33 Sequence name Weight Length Sequence name Weight Length
34 ------------- ------ ------ ------------- ------ ------
35 chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50
36 chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50
37 chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50
38 chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50
39 chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50
40 chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50
41 chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50
42 chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50
43 chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50
44 chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50
45 chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50
46 chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50
47 chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50
48 chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50
49 chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50
50 ********************************************************************************
51
52 ********************************************************************************
53 COMMAND LINE SUMMARY
54 ********************************************************************************
55 This information can also be useful in the event you wish to report a
56 problem with the MEME software.
57
58 command: meme /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat -o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1912/dataset_2530_files -nostatus
59
60 model: mod= zoops nmotifs= 1 evt= inf
61 object function= E-value of product of p-values
62 width: minw= 8 maxw= 50
63 width: wg= 11 ws= 1 endgaps= yes
64 nsites: minsites= 2 maxsites= 30 wnsites= 0.8
65 theta: spmap= pam spfuzz= 120
66 global: substring= yes branching= no wbranch= no
67 em: prior= megap b= 7500 maxiter= 50
68 distance= 1e-05
69 data: n= 1500 N= 30 shuffle= -1
70
71 sample: seed= 0 ctfrac= -1 maxwords= -1
72 Dirichlet mixture priors file: prior30.plib
73 Letter frequencies in dataset:
74 A 0.294 C 0.231 D 0.000 E 0.000 F 0.000 G 0.257 H 0.000 I 0.000 K 0.000
75 L 0.000 M 0.000 N 0.000 P 0.000 Q 0.000 R 0.000 S 0.000 T 0.217 V 0.000
76 W 0.000 Y 0.000
77 Background letter frequencies (from dataset with add-one prior applied):
78 A 0.291 C 0.229 D 0.001 E 0.001 F 0.001 G 0.255 H 0.001 I 0.001 K 0.001
79 L 0.001 M 0.001 N 0.001 P 0.001 Q 0.001 R 0.001 S 0.001 T 0.215 V 0.001
80 W 0.001 Y 0.001
81 ********************************************************************************
82
83
84 ********************************************************************************
85 MOTIF 1 MEME width = 11 sites = 25 llr = 239 E-value = 2.4e-011
86 ********************************************************************************
87 --------------------------------------------------------------------------------
88 Motif 1 Description
89 --------------------------------------------------------------------------------
90 Simplified A 2323:a:a8a8
91 pos.-specific C ::3::::::::
92 probability D :::::::::::
93 matrix E :::::::::::
94 F :::::::::::
95 G 7746::::::1
96 H :::::::::::
97 I :::::::::::
98 K :::::::::::
99 L :::::::::::
100 M :::::::::::
101 N :::::::::::
102 P :::::::::::
103 Q :::::::::::
104 R :::::::::::
105 S :::::::::::
106 T 1:2:a:a:2::
107 V :::::::::::
108 W :::::::::::
109 Y :::::::::::
110
111 bits 10.6
112 9.5
113 8.5
114 7.4
115 Relative 6.3
116 Entropy 5.3
117 (13.8 bits) 4.2
118 3.2
119 2.1 * **
120 1.1 ** ********
121 0.0 -----------
122
123 Multilevel GGGGTATAAAA
124 consensus AACA T
125 sequence
126
127
128 --------------------------------------------------------------------------------
129
130 --------------------------------------------------------------------------------
131 Motif 1 sites sorted by position p-value
132 --------------------------------------------------------------------------------
133 Sequence name Start P-value Site
134 ------------- ----- --------- -----------
135 chr21_46046964_46047014_ 13 1.06e-06 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC
136 chr21_46057197_46057247_ 37 3.41e-06 ACAGGCCCTG GGCATATAAAA GCC
137 chr21_45971413_45971463_ 10 3.41e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG
138 chr21_31964683_31964733_ 14 3.41e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC
139 chr21_45993530_45993580_ 8 4.00e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA
140 chr21_32202076_32202126_ 14 5.01e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC
141 chr21_46031920_46031970_ 16 6.06e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC
142 chr21_32410820_32410870_ 22 8.67e-06 AATCACTGAG GATGTATAAAA GTCCCAGGGA
143 chr21_32185595_32185645_ 19 8.67e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT
144 chr21_31992870_31992920_ 17 8.67e-06 CACTATTGAA GATGTATAAAA TTTCATTTGC
145 chr21_46020421_46020471_ 3 1.21e-05 GA GACATATAAAA GCCAACATCC
146 chr21_47517957_47518007_ 33 1.59e-05 CCGGCGGGGC GGGGTATAAAG GGGGCGG
147 chr21_45978668_45978718_ 5 1.59e-05 CAGA GGGGTATAAAG GTTCCGACCA
148 chr21_31914206_31914256_ 16 1.68e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG
149 chr21_32253899_32253949_ 20 2.03e-05 CACCAGCAAG GATATATAAAA GCTCAGGAGT
150 chr21_31744582_31744632_ 13 3.06e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC
151 chr21_19617074_19617124_ 40 3.06e-05 CCTCGGGACG TGGGTATATAA
152 chr21_45705687_45705737_ 38 3.82e-05 CGTGGTCGCG GGGGTATAACA GC
153 chr21_31768316_31768366_ 1 3.82e-05 . AACGTATATAA ATGGTCCTGT
154 chr21_47575506_47575556_ 31 4.02e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG
155 chr21_26934381_26934431_ 28 5.52e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG
156 chr21_31710037_31710087_ 15 5.94e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC
157 chr21_36411748_36411798_ 23 6.78e-05 AGTTTCAGTT GGCATCtaaaa attatataac
158 chr21_31933633_31933683_ 3 2.08e-04 TC AGAGTATATAT AAATGTTCCT
159 chr21_31962741_31962791_ 14 4.05e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC
160 --------------------------------------------------------------------------------
161
162 --------------------------------------------------------------------------------
163 Motif 1 block diagrams
164 --------------------------------------------------------------------------------
165 SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
166 ------------- ---------------- -------------
167 chr21_46046964_46047014_ 1.1e-06 12_[1]_27
168 chr21_46057197_46057247_ 3.4e-06 36_[1]_3
169 chr21_45971413_45971463_ 3.4e-06 9_[1]_30
170 chr21_31964683_31964733_ 3.4e-06 13_[1]_26
171 chr21_45993530_45993580_ 4e-06 7_[1]_32
172 chr21_32202076_32202126_ 5e-06 13_[1]_26
173 chr21_46031920_46031970_ 6.1e-06 15_[1]_24
174 chr21_32410820_32410870_ 8.7e-06 21_[1]_18
175 chr21_32185595_32185645_ 8.7e-06 18_[1]_21
176 chr21_31992870_31992920_ 8.7e-06 16_[1]_23
177 chr21_46020421_46020471_ 1.2e-05 2_[1]_37
178 chr21_47517957_47518007_ 1.6e-05 32_[1]_7
179 chr21_45978668_45978718_ 1.6e-05 4_[1]_35
180 chr21_31914206_31914256_ 1.7e-05 15_[1]_24
181 chr21_32253899_32253949_ 2e-05 19_[1]_20
182 chr21_31744582_31744632_ 3.1e-05 12_[1]_27
183 chr21_19617074_19617124_ 3.1e-05 39_[1]
184 chr21_45705687_45705737_ 3.8e-05 37_[1]_2
185 chr21_31768316_31768366_ 3.8e-05 [1]_39
186 chr21_47575506_47575556_ 4e-05 30_[1]_9
187 chr21_26934381_26934431_ 5.5e-05 27_[1]_12
188 chr21_31710037_31710087_ 5.9e-05 14_[1]_25
189 chr21_36411748_36411798_ 6.8e-05 22_[1]_17
190 chr21_31933633_31933683_ 0.00021 2_[1]_37
191 chr21_31962741_31962791_ 0.0004 13_[1]_26
192 --------------------------------------------------------------------------------
193
194 --------------------------------------------------------------------------------
195 Motif 1 in BLOCKS format
196 --------------------------------------------------------------------------------
197 BL MOTIF 1 width=11 seqs=25
198 chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1
199 chr21_46057197_46057247_ ( 37) GGCATATAAAA 1
200 chr21_45971413_45971463_ ( 10) GGCATATAAAA 1
201 chr21_31964683_31964733_ ( 14) GGCATATAAAA 1
202 chr21_45993530_45993580_ ( 8) GGAGTATAAAA 1
203 chr21_32202076_32202126_ ( 14) GAGGTATAAAA 1
204 chr21_46031920_46031970_ ( 16) AGGGTATAAAA 1
205 chr21_32410820_32410870_ ( 22) GATGTATAAAA 1
206 chr21_32185595_32185645_ ( 19) GGGATATATAA 1
207 chr21_31992870_31992920_ ( 17) GATGTATAAAA 1
208 chr21_46020421_46020471_ ( 3) GACATATAAAA 1
209 chr21_47517957_47518007_ ( 33) GGGGTATAAAG 1
210 chr21_45978668_45978718_ ( 5) GGGGTATAAAG 1
211 chr21_31914206_31914256_ ( 16) AGAGTATAAAA 1
212 chr21_32253899_32253949_ ( 20) GATATATAAAA 1
213 chr21_31744582_31744632_ ( 13) AGCATATATAA 1
214 chr21_19617074_19617124_ ( 40) TGGGTATATAA 1
215 chr21_45705687_45705737_ ( 38) GGGGTATAACA 1
216 chr21_31768316_31768366_ ( 1) AACGTATATAA 1
217 chr21_47575506_47575556_ ( 31) AGCGTATAAAG 1
218 chr21_26934381_26934431_ ( 28) GAGTTATAAAA 1
219 chr21_31710037_31710087_ ( 15) TGAGTATATAA 1
220 chr21_36411748_36411798_ ( 23) GGCATCTAAAA 1
221 chr21_31933633_31933683_ ( 3) AGAGTATATAT 1
222 chr21_31962741_31962791_ ( 14) GTTGGATAAAA 1
223 //
224
225 --------------------------------------------------------------------------------
226
227 --------------------------------------------------------------------------------
228 Motif 1 position-specific scoring matrix
229 --------------------------------------------------------------------------------
230 log-odds matrix: alength= 20 w= 11 n= 1200 bayes= 5.33554 E= 2.4e-011
231 -32 -680 91 77 7 138 -20 55 64 107 11 150 142 72 87 396 -148 221 -140 -36
232 -11 -680 89 76 7 137 -21 55 63 107 10 149 141 71 87 396 -239 220 -140 -36
233 -79 41 4 21 -7 44 -62 42 -5 99 0 99 138 52 42 399 -46 223 -173 -68
234 11 -677 48 47 -2 127 -43 46 27 101 3 124 138 60 62 397 -235 220 -160 -55
235 -596 -820 12 -21 -53 -267 -74 37 16 44 -37 98 31 9 19 319 212 127 -193 -95
236 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8
237 -838 -990 -89 -149 -151 -841 -161 -117 -113 -66 -209 -68 -69 -129 -91 111 221 -55 -255 -173
238 176 -858 -79 -103 -115 -717 -148 -95 -108 -17 -162 -61 -12 -95 -69 193 -737 52 -240 -153
239 134 -686 0 16 -12 -553 -68 44 -8 96 -9 88 124 41 36 384 11 216 -177 -71
240 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8
241 147 -614 89 129 93 -121 12 160 113 217 108 144 144 111 125 447 -241 332 -81 22
242 --------------------------------------------------------------------------------
243
244 --------------------------------------------------------------------------------
245 Motif 1 position-specific probability matrix
246 --------------------------------------------------------------------------------
247 letter-probability matrix: alength= 20 w= 11 nsites= 25 E= 2.4e-011
248 0.240000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.080000 0.000000 0.000000 0.000000
249 0.280000 0.000000 0.000000 0.000000 0.000000 0.680000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000
250 0.160000 0.320000 0.000000 0.000000 0.000000 0.360000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.160000 0.000000 0.000000 0.000000
251 0.320000 0.000000 0.000000 0.000000 0.000000 0.640000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000
252 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.960000 0.000000 0.000000 0.000000
253 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
254 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000
255 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
256 0.760000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.240000 0.000000 0.000000 0.000000
257 0.960000 0.040000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
258 0.840000 0.000000 0.000000 0.000000 0.000000 0.120000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.040000 0.000000 0.000000 0.000000
259 --------------------------------------------------------------------------------
260
261 --------------------------------------------------------------------------------
262 Motif 1 regular expression
263 --------------------------------------------------------------------------------
264 [GA][GA][GC][GA]TATA[AT]AA
265 --------------------------------------------------------------------------------
266
267
268
269
270 Time 0.53 secs.
271
272 ********************************************************************************
273
274
275 ********************************************************************************
276 SUMMARY OF MOTIFS
277 ********************************************************************************
278
279 --------------------------------------------------------------------------------
280 Combined block diagrams: non-overlapping sites with p-value < 0.0001
281 --------------------------------------------------------------------------------
282 SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
283 ------------- ---------------- -------------
284 chr21_19617074_19617124_ 1.22e-03 39_[1(3.06e-05)]
285 chr21_26934381_26934431_ 2.21e-03 27_[1(5.52e-05)]_12
286 chr21_28217753_28217803_ 7.29e-01 50
287 chr21_31710037_31710087_ 2.37e-03 14_[1(5.94e-05)]_25
288 chr21_31744582_31744632_ 1.22e-03 12_[1(3.06e-05)]_27
289 chr21_31768316_31768366_ 1.53e-03 [1(3.82e-05)]_39
290 chr21_31914206_31914256_ 6.70e-04 15_[1(1.68e-05)]_24
291 chr21_31933633_31933683_ 1.81e-03 4_[1(4.54e-05)]_35
292 chr21_31962741_31962791_ 1.61e-02 50
293 chr21_31964683_31964733_ 1.36e-04 13_[1(3.41e-06)]_26
294 chr21_31973364_31973414_ 1.99e-01 50
295 chr21_31992870_31992920_ 3.47e-04 16_[1(8.67e-06)]_23
296 chr21_32185595_32185645_ 3.47e-04 18_[1(8.67e-06)]_21
297 chr21_32202076_32202126_ 2.01e-04 13_[1(5.01e-06)]_26
298 chr21_32253899_32253949_ 8.11e-04 19_[1(2.03e-05)]_20
299 chr21_32410820_32410870_ 3.47e-04 21_[1(8.67e-06)]_18
300 chr21_36411748_36411798_ 2.71e-03 22_[1(6.78e-05)]_17
301 chr21_37838750_37838800_ 8.23e-02 50
302 chr21_45705687_45705737_ 1.53e-03 37_[1(3.82e-05)]_2
303 chr21_45971413_45971463_ 1.36e-04 9_[1(3.41e-06)]_30
304 chr21_45978668_45978718_ 6.37e-04 4_[1(1.59e-05)]_35
305 chr21_45993530_45993580_ 1.60e-04 7_[1(4.00e-06)]_32
306 chr21_46020421_46020471_ 4.83e-04 2_[1(1.21e-05)]_37
307 chr21_46031920_46031970_ 2.43e-04 15_[1(6.06e-06)]_24
308 chr21_46046964_46047014_ 4.26e-05 12_[1(1.06e-06)]_27
309 chr21_46057197_46057247_ 1.36e-04 36_[1(3.41e-06)]_3
310 chr21_46086869_46086919_ 4.30e-02 50
311 chr21_46102103_46102153_ 4.30e-02 50
312 chr21_47517957_47518007_ 6.37e-04 32_[1(1.59e-05)]_7
313 chr21_47575506_47575556_ 1.61e-03 30_[1(4.02e-05)]_9
314 --------------------------------------------------------------------------------
315
316 ********************************************************************************
317
318
319 ********************************************************************************
320 Stopped because requested number of motifs (1) found.
321 ********************************************************************************
322
323 CPU: MacBook-Pro-2.local
324
325 ********************************************************************************