Mercurial > repos > iuc > meme_psp_gen
diff test-data/meme_output_test1.txt @ 3:ff2f53a32d0e draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
| author | iuc |
|---|---|
| date | Wed, 11 Dec 2019 18:04:34 -0500 |
| parents | b48e673af4e8 |
| children | 5f95d385a33c |
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--- a/test-data/meme_output_test1.txt Thu May 17 14:11:15 2018 -0400 +++ b/test-data/meme_output_test1.txt Wed Dec 11 18:04:34 2019 -0500 @@ -1,325 +1,61 @@ ******************************************************************************** MEME - Motif discovery tool -******************************************************************************** -MEME version 4.12.0 (Release date: Tue Jun 27 16:22:50 2017 -0700) - -For further information on how to interpret these results or to get -a copy of the MEME software please access http://meme-suite.org . - -This file may be used as input to the MAST algorithm for searching -sequence databases for matches to groups of motifs. MAST is available -for interactive use and downloading at http://meme-suite.org . -******************************************************************************** - - -******************************************************************************** +MEME version 5.0.5 (Release date: Mon Mar 18 20:12:19 2019 -0700) REFERENCE -******************************************************************************** -If you use this program in your research, please cite: - -Timothy L. Bailey and Charles Elkan, -"Fitting a mixture model by expectation maximization to discover -motifs in biopolymers", Proceedings of the Second International -Conference on Intelligent Systems for Molecular Biology, pp. 28-36, -AAAI Press, Menlo Park, California, 1994. -******************************************************************************** - - -******************************************************************************** TRAINING SET -******************************************************************************** -DATAFILE= meme_input_1.fasta +CONTROL SEQUENCES= --none-- ALPHABET= ACDEFGHIKLMNPQRSTVWY Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ chr21_19617074_19617124_ 1.0000 50 chr21_26934381_26934431_ 1.0000 50 -chr21_28217753_28217803_ 1.0000 50 chr21_31710037_31710087_ 1.0000 50 -chr21_31744582_31744632_ 1.0000 50 chr21_31768316_31768366_ 1.0000 50 -chr21_31914206_31914256_ 1.0000 50 chr21_31933633_31933683_ 1.0000 50 -chr21_31962741_31962791_ 1.0000 50 chr21_31964683_31964733_ 1.0000 50 -chr21_31973364_31973414_ 1.0000 50 chr21_31992870_31992920_ 1.0000 50 -chr21_32185595_32185645_ 1.0000 50 chr21_32202076_32202126_ 1.0000 50 -chr21_32253899_32253949_ 1.0000 50 chr21_32410820_32410870_ 1.0000 50 -chr21_36411748_36411798_ 1.0000 50 chr21_37838750_37838800_ 1.0000 50 -chr21_45705687_45705737_ 1.0000 50 chr21_45971413_45971463_ 1.0000 50 -chr21_45978668_45978718_ 1.0000 50 chr21_45993530_45993580_ 1.0000 50 -chr21_46020421_46020471_ 1.0000 50 chr21_46031920_46031970_ 1.0000 50 -chr21_46046964_46047014_ 1.0000 50 chr21_46057197_46057247_ 1.0000 50 -chr21_46086869_46086919_ 1.0000 50 chr21_46102103_46102153_ 1.0000 50 -chr21_47517957_47518007_ 1.0000 50 chr21_47575506_47575556_ 1.0000 50 -******************************************************************************** - -******************************************************************************** COMMAND LINE SUMMARY -******************************************************************************** -This information can also be useful in the event you wish to report a -problem with the MEME software. - -command: meme meme_input_1.fasta -o meme_test1_out -nostatus -maxsize 1000000 - model: mod= zoops nmotifs= 1 evt= inf -object function= E-value of product of p-values +objective function: em= E-value of product of p-values + starts= E-value of product of p-values width: minw= 8 maxw= 50 -width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 30 wnsites= 0.8 theta: spmap= pam spfuzz= 120 -global: substring= yes branching= no wbranch= no em: prior= megap b= 7500 maxiter= 50 distance= 1e-05 -data: n= 1500 N= 30 shuffle= -1 - -sample: seed= 0 ctfrac= -1 maxwords= -1 +trim: wg= 11 ws= 1 endgaps= yes +data: n= 1500 N= 30 +sample: seed= 0 hsfrac= 0 + searchsize= 1500 norand= no csites= 1000 Dirichlet mixture priors file: prior30.plib Letter frequencies in dataset: -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 -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 -W 0.000 Y 0.000 -Background letter frequencies (from dataset with add-one prior applied): -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 -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 -W 0.001 Y 0.001 -******************************************************************************** - - -******************************************************************************** +A 0.294 C 0.231 D 0 E 0 F 0 G 0.257 H 0 I 0 K 0 +L 0 M 0 N 0 P 0 Q 0 R 0 S 0 T 0.217 V 0 +W 0 Y 0 +Background letter frequencies (from file dataset with add-one prior applied): +A 0.291 C 0.229 D 0.000658 E 0.000658 F 0.000658 G 0.255 H 0.000658 I 0.000658 K 0.000658 +L 0.000658 M 0.000658 N 0.000658 P 0.000658 Q 0.000658 R 0.000658 S 0.000658 T 0.215 V 0.000658 +W 0.000658 Y 0.000658 +Background model order: 0 MOTIF GGGGTATAAAA MEME-1 width = 11 sites = 25 llr = 239 E-value = 2.4e-011 -******************************************************************************** -------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 Description --------------------------------------------------------------------------------- -Simplified A 2323:a:a8a8 -pos.-specific C ::3:::::::: -probability D ::::::::::: -matrix E ::::::::::: - F ::::::::::: - G 7746::::::1 - H ::::::::::: - I ::::::::::: - K ::::::::::: - L ::::::::::: - M ::::::::::: - N ::::::::::: - P ::::::::::: - Q ::::::::::: - R ::::::::::: - S ::::::::::: - T 1:2:a:a:2:: - V ::::::::::: - W ::::::::::: - Y ::::::::::: - - bits 10.6 - 9.5 - 8.5 - 7.4 -Relative 6.3 -Entropy 5.3 -(13.8 bits) 4.2 - 3.2 - 2.1 * ** - 1.1 ** ******** - 0.0 ----------- - -Multilevel GGGGTATAAAA -consensus AACA T -sequence - - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 sites sorted by position p-value --------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------- chr21_46046964_46047014_ 13 1.06e-06 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC -chr21_46057197_46057247_ 37 3.41e-06 ACAGGCCCTG GGCATATAAAA GCC -chr21_45971413_45971463_ 10 3.41e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG -chr21_31964683_31964733_ 14 3.41e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC -chr21_45993530_45993580_ 8 4.00e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA -chr21_32202076_32202126_ 14 5.01e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC -chr21_46031920_46031970_ 16 6.06e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC -chr21_32410820_32410870_ 22 8.67e-06 AATCACTGAG GATGTATAAAA GTCCCAGGGA -chr21_32185595_32185645_ 19 8.67e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT -chr21_31992870_31992920_ 17 8.67e-06 CACTATTGAA GATGTATAAAA TTTCATTTGC -chr21_46020421_46020471_ 3 1.21e-05 GA GACATATAAAA GCCAACATCC -chr21_47517957_47518007_ 33 1.59e-05 CCGGCGGGGC GGGGTATAAAG GGGGCGG -chr21_45978668_45978718_ 5 1.59e-05 CAGA GGGGTATAAAG GTTCCGACCA -chr21_31914206_31914256_ 16 1.68e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG -chr21_32253899_32253949_ 20 2.03e-05 CACCAGCAAG GATATATAAAA GCTCAGGAGT -chr21_31744582_31744632_ 13 3.06e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC -chr21_19617074_19617124_ 40 3.06e-05 CCTCGGGACG TGGGTATATAA -chr21_45705687_45705737_ 38 3.82e-05 CGTGGTCGCG GGGGTATAACA GC -chr21_31768316_31768366_ 1 3.82e-05 . AACGTATATAA ATGGTCCTGT -chr21_47575506_47575556_ 31 4.02e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG -chr21_26934381_26934431_ 28 5.52e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG -chr21_31710037_31710087_ 15 5.94e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC -chr21_36411748_36411798_ 23 6.78e-05 AGTTTCAGTT GGCATCtaaaa attatataac -chr21_31933633_31933683_ 3 2.08e-04 TC AGAGTATATAT AAATGTTCCT -chr21_31962741_31962791_ 14 4.05e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 block diagrams --------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr21_46046964_46047014_ 1.1e-06 12_[1]_27 -chr21_46057197_46057247_ 3.4e-06 36_[1]_3 -chr21_45971413_45971463_ 3.4e-06 9_[1]_30 -chr21_31964683_31964733_ 3.4e-06 13_[1]_26 -chr21_45993530_45993580_ 4e-06 7_[1]_32 -chr21_32202076_32202126_ 5e-06 13_[1]_26 -chr21_46031920_46031970_ 6.1e-06 15_[1]_24 -chr21_32410820_32410870_ 8.7e-06 21_[1]_18 -chr21_32185595_32185645_ 8.7e-06 18_[1]_21 -chr21_31992870_31992920_ 8.7e-06 16_[1]_23 -chr21_46020421_46020471_ 1.2e-05 2_[1]_37 -chr21_47517957_47518007_ 1.6e-05 32_[1]_7 -chr21_45978668_45978718_ 1.6e-05 4_[1]_35 -chr21_31914206_31914256_ 1.7e-05 15_[1]_24 -chr21_32253899_32253949_ 2e-05 19_[1]_20 -chr21_31744582_31744632_ 3.1e-05 12_[1]_27 -chr21_19617074_19617124_ 3.1e-05 39_[1] -chr21_45705687_45705737_ 3.8e-05 37_[1]_2 -chr21_31768316_31768366_ 3.8e-05 [1]_39 -chr21_47575506_47575556_ 4e-05 30_[1]_9 -chr21_26934381_26934431_ 5.5e-05 27_[1]_12 -chr21_31710037_31710087_ 5.9e-05 14_[1]_25 -chr21_36411748_36411798_ 6.8e-05 22_[1]_17 -chr21_31933633_31933683_ 0.00021 2_[1]_37 -chr21_31962741_31962791_ 0.0004 13_[1]_26 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 in BLOCKS format --------------------------------------------------------------------------------- BL MOTIF GGGGTATAAAA width=11 seqs=25 chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1 -chr21_46057197_46057247_ ( 37) GGCATATAAAA 1 -chr21_45971413_45971463_ ( 10) GGCATATAAAA 1 -chr21_31964683_31964733_ ( 14) GGCATATAAAA 1 -chr21_45993530_45993580_ ( 8) GGAGTATAAAA 1 -chr21_32202076_32202126_ ( 14) GAGGTATAAAA 1 -chr21_46031920_46031970_ ( 16) AGGGTATAAAA 1 -chr21_32410820_32410870_ ( 22) GATGTATAAAA 1 -chr21_32185595_32185645_ ( 19) GGGATATATAA 1 -chr21_31992870_31992920_ ( 17) GATGTATAAAA 1 -chr21_46020421_46020471_ ( 3) GACATATAAAA 1 -chr21_47517957_47518007_ ( 33) GGGGTATAAAG 1 -chr21_45978668_45978718_ ( 5) GGGGTATAAAG 1 -chr21_31914206_31914256_ ( 16) AGAGTATAAAA 1 -chr21_32253899_32253949_ ( 20) GATATATAAAA 1 -chr21_31744582_31744632_ ( 13) AGCATATATAA 1 -chr21_19617074_19617124_ ( 40) TGGGTATATAA 1 -chr21_45705687_45705737_ ( 38) GGGGTATAACA 1 -chr21_31768316_31768366_ ( 1) AACGTATATAA 1 -chr21_47575506_47575556_ ( 31) AGCGTATAAAG 1 -chr21_26934381_26934431_ ( 28) GAGTTATAAAA 1 -chr21_31710037_31710087_ ( 15) TGAGTATATAA 1 -chr21_36411748_36411798_ ( 23) GGCATCTAAAA 1 -chr21_31933633_31933683_ ( 3) AGAGTATATAT 1 -chr21_31962741_31962791_ ( 14) GTTGGATAAAA 1 -// - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 position-specific scoring matrix --------------------------------------------------------------------------------- log-odds matrix: alength= 20 w= 11 n= 1200 bayes= 5.33554 E= 2.4e-011 -32 -680 91 77 7 138 -20 55 64 107 11 150 142 72 87 396 -148 221 -140 -36 - -11 -680 89 76 7 137 -21 55 63 107 10 149 141 71 87 396 -239 220 -140 -36 - -79 41 4 21 -7 44 -62 42 -5 99 0 99 138 52 42 399 -46 223 -173 -68 - 11 -677 48 47 -2 127 -43 46 27 101 3 124 138 60 62 397 -235 220 -160 -55 - -596 -820 12 -21 -53 -267 -74 37 16 44 -37 98 31 9 19 319 212 127 -193 -95 - 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8 - -838 -990 -89 -149 -151 -841 -161 -117 -113 -66 -209 -68 -69 -129 -91 111 221 -55 -255 -173 - 176 -858 -79 -103 -115 -717 -148 -95 -108 -17 -162 -61 -12 -95 -69 193 -737 52 -240 -153 - 134 -686 0 16 -12 -553 -68 44 -8 96 -9 88 124 41 36 384 11 216 -177 -71 - 165 -261 70 110 77 -521 -4 147 95 201 90 121 124 91 107 425 -527 314 -95 8 - 147 -614 89 129 93 -121 12 160 113 217 108 144 144 111 125 447 -241 332 -81 22 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 position-specific probability matrix --------------------------------------------------------------------------------- letter-probability matrix: alength= 20 w= 11 nsites= 25 E= 2.4e-011 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- Motif GGGGTATAAAA MEME-1 regular expression --------------------------------------------------------------------------------- [GA][GA][GC][GA]TATA[AT]AA --------------------------------------------------------------------------------- - - - - -Time 0.77 secs. - -******************************************************************************** - - -******************************************************************************** SUMMARY OF MOTIFS -******************************************************************************** - --------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 --------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr21_19617074_19617124_ 1.22e-03 39_[1(3.06e-05)] -chr21_26934381_26934431_ 2.21e-03 27_[1(5.52e-05)]_12 -chr21_28217753_28217803_ 7.29e-01 50 -chr21_31710037_31710087_ 2.37e-03 14_[1(5.94e-05)]_25 -chr21_31744582_31744632_ 1.22e-03 12_[1(3.06e-05)]_27 -chr21_31768316_31768366_ 1.53e-03 [1(3.82e-05)]_39 -chr21_31914206_31914256_ 6.70e-04 15_[1(1.68e-05)]_24 -chr21_31933633_31933683_ 1.81e-03 4_[1(4.54e-05)]_35 -chr21_31962741_31962791_ 1.61e-02 50 -chr21_31964683_31964733_ 1.36e-04 13_[1(3.41e-06)]_26 -chr21_31973364_31973414_ 1.99e-01 50 -chr21_31992870_31992920_ 3.47e-04 16_[1(8.67e-06)]_23 -chr21_32185595_32185645_ 3.47e-04 18_[1(8.67e-06)]_21 -chr21_32202076_32202126_ 2.01e-04 13_[1(5.01e-06)]_26 -chr21_32253899_32253949_ 8.11e-04 19_[1(2.03e-05)]_20 -chr21_32410820_32410870_ 3.47e-04 21_[1(8.67e-06)]_18 -chr21_36411748_36411798_ 2.71e-03 22_[1(6.78e-05)]_17 -chr21_37838750_37838800_ 8.23e-02 50 -chr21_45705687_45705737_ 1.53e-03 37_[1(3.82e-05)]_2 -chr21_45971413_45971463_ 1.36e-04 9_[1(3.41e-06)]_30 -chr21_45978668_45978718_ 6.37e-04 4_[1(1.59e-05)]_35 -chr21_45993530_45993580_ 1.60e-04 7_[1(4.00e-06)]_32 -chr21_46020421_46020471_ 4.83e-04 2_[1(1.21e-05)]_37 -chr21_46031920_46031970_ 2.43e-04 15_[1(6.06e-06)]_24 -chr21_46046964_46047014_ 4.26e-05 12_[1(1.06e-06)]_27 -chr21_46057197_46057247_ 1.36e-04 36_[1(3.41e-06)]_3 -chr21_46086869_46086919_ 4.30e-02 50 -chr21_46102103_46102153_ 4.30e-02 50 -chr21_47517957_47518007_ 6.37e-04 32_[1(1.59e-05)]_7 -chr21_47575506_47575556_ 1.61e-03 30_[1(4.02e-05)]_9 --------------------------------------------------------------------------------- - -******************************************************************************** - - -******************************************************************************** Stopped because requested number of motifs (1) found. -******************************************************************************** - -CPU: ThinkPad-T450s - -********************************************************************************