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
line wrap: on
line diff
--- 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
-
-********************************************************************************