diff test-data/meme_output_test1.txt @ 13:57e5d9382f36 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e2cf796f991cbe8c96e0cc5a0056b7255ac3ad6b
author iuc
date Thu, 17 May 2018 14:10:48 -0400
parents
children 3f0dd362b755
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/meme_output_test1.txt	Thu May 17 14:10:48 2018 -0400
@@ -0,0 +1,325 @@
+********************************************************************************
+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 .
+********************************************************************************
+
+
+********************************************************************************
+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
+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
+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 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
+
+********************************************************************************