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

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
parents
children eca84de658b0
line wrap: on
line source

********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 4.11.0 (Release date: Thu Nov 26 17:48:49 2015 +1000)

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 .
********************************************************************************


********************************************************************************
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= /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat
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 /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 

model:  mod=         zoops    nmotifs=         1    evt=           inf
object function=  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
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 
********************************************************************************


********************************************************************************
MOTIF  1 MEME	width =  11  sites =  25  llr = 239  E-value = 2.4e-011
********************************************************************************
--------------------------------------------------------------------------------
	Motif 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 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 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 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 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 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 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 1 regular expression
--------------------------------------------------------------------------------
[GA][GA][GC][GA]TATA[AT]AA
--------------------------------------------------------------------------------




Time  0.53 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: MacBook-Pro-2.local

********************************************************************************