Mercurial > repos > iuc > meme_meme
diff test-data/meme_output_test2.txt @ 14:3f0dd362b755 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit 86a94f48321780dbe18ef5b099434c347ec2f4d0"
| author | iuc |
|---|---|
| date | Wed, 11 Dec 2019 18:05:15 -0500 |
| parents | 57e5d9382f36 |
| children | 19237efe98d1 |
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--- a/test-data/meme_output_test2.txt Thu May 17 14:10:48 2018 -0400 +++ b/test-data/meme_output_test2.txt Wed Dec 11 18:05:15 2019 -0500 @@ -1,88 +1,36 @@ ******************************************************************************** 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= Galaxy_FASTA_Input +PRIMARY SEQUENCES= Galaxy_FASTA_Input +CONTROL SEQUENCES= --none-- ALPHABET= ACGT 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_test2_out -nostatus -maxsize 1000000 -sf Galaxy_FASTA_Input -dna -mod zoops -nmotifs 1 -wnsites 0.8 -minw 8 -maxw 50 -wg 11 -ws 1 -maxiter 50 -distance 0.001 -prior dirichlet -b 0.01 -plib prior30.plib -spmap uni -spfuzz 0.5 - 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 +strands: + width: minw= 8 maxw= 50 -width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 30 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 -global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 0.001 -data: n= 1500 N= 30 shuffle= -1 -strands: + -sample: seed= 0 ctfrac= -1 maxwords= -1 -Dirichlet mixture priors file: prior30.plib +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: Letter frequencies in dataset: A 0.294 C 0.231 G 0.257 T 0.217 -Background letter frequencies (from dataset with add-one prior applied): +Background letter frequencies (from file dataset with add-one prior applied): A 0.294 C 0.231 G 0.257 T 0.217 -******************************************************************************** - - -******************************************************************************** +Background model order: 0 MOTIF GGSRTATAAAA MEME-1 width = 11 sites = 30 llr = 254 E-value = 5.1e-040 -******************************************************************************** --------------------------------------------------------------------------------- Motif GGSRTATAAAA MEME-1 Description --------------------------------------------------------------------------------- Simplified A 3313:9:a798 pos.-specific C 1:3::1:::1: probability G 6756::::::2 @@ -103,124 +51,17 @@ Multilevel GGGGTATAAAA consensus AACA T sequence - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- Motif GGSRTATAAAA MEME-1 sites sorted by position p-value --------------------------------------------------------------------------------- Sequence name Start P-value Site -------------- ----- --------- ----------- chr21_46046964_46047014_ 13 4.51e-07 AAGGCCAGGA GGGGTATAAAA GCCTGAGAGC -chr21_46031920_46031970_ 16 2.22e-06 ATACCCAGGG AGGGTATAAAA CCTCAGCAGC -chr21_32202076_32202126_ 14 2.74e-06 CCACCAGCTT GAGGTATAAAA AGCCCTGTAC -chr21_46057197_46057247_ 37 4.86e-06 ACAGGCCCTG GGCATATAAAA GCC -chr21_45993530_45993580_ 8 4.86e-06 CCAAGGA GGAGTATAAAA GCCCCACAAA -chr21_45971413_45971463_ 10 4.86e-06 CAGGCCCTG GGCATATAAAA GCCCCAGCAG -chr21_31964683_31964733_ 14 4.86e-06 GATTCACTGA GGCATATAAAA GGCCCTCTGC -chr21_47517957_47518007_ 33 6.48e-06 CCGGCGGGGC GGGGTATAAAG GGGGCGG -chr21_45978668_45978718_ 5 6.48e-06 CAGA GGGGTATAAAG GTTCCGACCA -chr21_32185595_32185645_ 19 6.48e-06 CACCAGAGCT GGGATATATAA AGAAGGTTCT -chr21_32410820_32410870_ 22 1.38e-05 AATCACTGAG GATGTATAAAA GTCCCAGGGA -chr21_31992870_31992920_ 17 1.38e-05 CACTATTGAA GATGTATAAAA TTTCATTTGC -chr21_19617074_19617124_ 40 1.41e-05 CCTCGGGACG TGGGTATATAA -chr21_31914206_31914256_ 16 1.61e-05 CCCACTACTT AGAGTATAAAA TCATTCTGAG -chr21_46020421_46020471_ 3 1.95e-05 GA GACATATAAAA GCCAACATCC -chr21_32253899_32253949_ 18 1.95e-05 CCCACCAGCA AGGATATATAA AAGCTCAGGA -chr21_45705687_45705737_ 38 2.16e-05 CGTGGTCGCG GGGGTATAACA GC -chr21_47575506_47575556_ 31 3.04e-05 GCTGCCGGTG AGCGTATAAAG GCCCTGGCG -chr21_31744582_31744632_ 13 3.04e-05 CAGGTCTAAG AGCATATATAA CTTGGAGTCC -chr21_31768316_31768366_ 1 3.67e-05 . AACGTATATAA ATGGTCCTGT -chr21_26934381_26934431_ 28 3.93e-05 AGTCACAAGT GAGTTATAAAA GGGTCGCACG -chr21_31933633_31933683_ 5 5.65e-05 TCAG AGTATATATAA ATGTTCCTGT -chr21_31710037_31710087_ 15 6.24e-05 CCCAGGTTTC TGAGTATATAA TCGCCGCACC -chr21_36411748_36411798_ 23 7.15e-05 AGTTTCAGTT GGCATCtaaaa attatataac -chr21_46102103_46102153_ 37 1.39e-04 TGCCTGGGTC CAGGTATAAAG GCT -chr21_46086869_46086919_ 38 1.39e-04 TGCCTGGGCC CAGGTATAAAG GC -chr21_37838750_37838800_ 3 4.81e-04 ga tggttttataa ggggcctcac -chr21_31962741_31962791_ 14 8.57e-04 TATAACTCAG GTTGGATAAAA TAATTTGTAC -chr21_31973364_31973414_ 8 1.47e-03 aaactta aaactctataa acttaaaact -chr21_28217753_28217803_ 27 2.64e-03 GGTGGGGGTG GGGGTTTCACT GGTCCACTAT --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- Motif GGSRTATAAAA MEME-1 block diagrams --------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- chr21_46046964_46047014_ 4.5e-07 12_[+1]_27 -chr21_46031920_46031970_ 2.2e-06 15_[+1]_24 -chr21_32202076_32202126_ 2.7e-06 13_[+1]_26 -chr21_46057197_46057247_ 4.9e-06 36_[+1]_3 -chr21_45993530_45993580_ 4.9e-06 7_[+1]_32 -chr21_45971413_45971463_ 4.9e-06 9_[+1]_30 -chr21_31964683_31964733_ 4.9e-06 13_[+1]_26 -chr21_47517957_47518007_ 6.5e-06 32_[+1]_7 -chr21_45978668_45978718_ 6.5e-06 4_[+1]_35 -chr21_32185595_32185645_ 6.5e-06 18_[+1]_21 -chr21_32410820_32410870_ 1.4e-05 21_[+1]_18 -chr21_31992870_31992920_ 1.4e-05 16_[+1]_23 -chr21_19617074_19617124_ 1.4e-05 39_[+1] -chr21_31914206_31914256_ 1.6e-05 15_[+1]_24 -chr21_46020421_46020471_ 1.9e-05 2_[+1]_37 -chr21_32253899_32253949_ 1.9e-05 17_[+1]_22 -chr21_45705687_45705737_ 2.2e-05 37_[+1]_2 -chr21_47575506_47575556_ 3e-05 30_[+1]_9 -chr21_31744582_31744632_ 3e-05 12_[+1]_27 -chr21_31768316_31768366_ 3.7e-05 [+1]_39 -chr21_26934381_26934431_ 3.9e-05 27_[+1]_12 -chr21_31933633_31933683_ 5.6e-05 4_[+1]_35 -chr21_31710037_31710087_ 6.2e-05 14_[+1]_25 -chr21_36411748_36411798_ 7.1e-05 22_[+1]_17 -chr21_46102103_46102153_ 0.00014 36_[+1]_3 -chr21_46086869_46086919_ 0.00014 37_[+1]_2 -chr21_37838750_37838800_ 0.00048 2_[+1]_37 -chr21_31962741_31962791_ 0.00086 13_[+1]_26 -chr21_31973364_31973414_ 0.0015 7_[+1]_32 -chr21_28217753_28217803_ 0.0026 26_[+1]_13 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- Motif GGSRTATAAAA MEME-1 in BLOCKS format --------------------------------------------------------------------------------- BL MOTIF GGSRTATAAAA width=11 seqs=30 chr21_46046964_46047014_ ( 13) GGGGTATAAAA 1 -chr21_46031920_46031970_ ( 16) AGGGTATAAAA 1 -chr21_32202076_32202126_ ( 14) GAGGTATAAAA 1 -chr21_46057197_46057247_ ( 37) GGCATATAAAA 1 -chr21_45993530_45993580_ ( 8) GGAGTATAAAA 1 -chr21_45971413_45971463_ ( 10) GGCATATAAAA 1 -chr21_31964683_31964733_ ( 14) GGCATATAAAA 1 -chr21_47517957_47518007_ ( 33) GGGGTATAAAG 1 -chr21_45978668_45978718_ ( 5) GGGGTATAAAG 1 -chr21_32185595_32185645_ ( 19) GGGATATATAA 1 -chr21_32410820_32410870_ ( 22) GATGTATAAAA 1 -chr21_31992870_31992920_ ( 17) GATGTATAAAA 1 -chr21_19617074_19617124_ ( 40) TGGGTATATAA 1 -chr21_31914206_31914256_ ( 16) AGAGTATAAAA 1 -chr21_46020421_46020471_ ( 3) GACATATAAAA 1 -chr21_32253899_32253949_ ( 18) AGGATATATAA 1 -chr21_45705687_45705737_ ( 38) GGGGTATAACA 1 -chr21_47575506_47575556_ ( 31) AGCGTATAAAG 1 -chr21_31744582_31744632_ ( 13) AGCATATATAA 1 -chr21_31768316_31768366_ ( 1) AACGTATATAA 1 -chr21_26934381_26934431_ ( 28) GAGTTATAAAA 1 -chr21_31933633_31933683_ ( 5) AGTATATATAA 1 -chr21_31710037_31710087_ ( 15) TGAGTATATAA 1 -chr21_36411748_36411798_ ( 23) GGCATCTAAAA 1 -chr21_46102103_46102153_ ( 37) CAGGTATAAAG 1 -chr21_46086869_46086919_ ( 38) CAGGTATAAAG 1 -chr21_37838750_37838800_ ( 3) TGGTTTTATAA 1 -chr21_31962741_31962791_ ( 14) GTTGGATAAAA 1 -chr21_31973364_31973414_ ( 8) AAACTCTATAA 1 -chr21_28217753_28217803_ ( 27) GGGGTTTCACT 1 -// - --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- Motif GGSRTATAAAA MEME-1 position-specific scoring matrix --------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1200 bayes= 5.2854 E= 5.1e-040 -14 -179 114 -112 3 -1155 137 -270 @@ -233,87 +74,13 @@ 125 -1155 -1155 46 167 -179 -1155 -1155 144 -1155 -63 -270 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- Motif GGSRTATAAAA MEME-1 position-specific probability matrix --------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 30 E= 5.1e-040 0.266667 0.066667 0.566667 0.100000 - 0.300000 0.000000 0.666667 0.033333 - 0.133333 0.266667 0.466667 0.133333 - 0.300000 0.033333 0.600000 0.066667 - 0.000000 0.000000 0.033333 0.966667 - 0.866667 0.066667 0.000000 0.066667 - 0.000000 0.000000 0.000000 1.000000 - 0.966667 0.033333 0.000000 0.000000 - 0.700000 0.000000 0.000000 0.300000 - 0.933333 0.066667 0.000000 0.000000 - 0.800000 0.000000 0.166667 0.033333 --------------------------------------------------------------------------------- - --------------------------------------------------------------------------------- Motif GGSRTATAAAA MEME-1 regular expression --------------------------------------------------------------------------------- [GA][GA][GC][GA]TATA[AT]AA --------------------------------------------------------------------------------- - - - - -Time 0.38 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_ 5.63e-04 39_[+1(1.41e-05)] -chr21_26934381_26934431_ 1.57e-03 27_[+1(3.93e-05)]_12 -chr21_28217753_28217803_ 1.00e-01 50 -chr21_31710037_31710087_ 2.49e-03 14_[+1(6.24e-05)]_25 -chr21_31744582_31744632_ 1.22e-03 12_[+1(3.04e-05)]_27 -chr21_31768316_31768366_ 1.47e-03 [+1(3.67e-05)]_39 -chr21_31914206_31914256_ 6.45e-04 15_[+1(1.61e-05)]_24 -chr21_31933633_31933683_ 2.26e-03 4_[+1(5.65e-05)]_35 -chr21_31962741_31962791_ 3.37e-02 50 -chr21_31964683_31964733_ 1.95e-04 13_[+1(4.86e-06)]_26 -chr21_31973364_31973414_ 5.73e-02 50 -chr21_31992870_31992920_ 5.52e-04 16_[+1(1.38e-05)]_23 -chr21_32185595_32185645_ 2.59e-04 18_[+1(6.48e-06)]_21 -chr21_32202076_32202126_ 1.10e-04 13_[+1(2.74e-06)]_26 -chr21_32253899_32253949_ 7.78e-04 17_[+1(1.95e-05)]_22 -chr21_32410820_32410870_ 5.52e-04 21_[+1(1.38e-05)]_18 -chr21_36411748_36411798_ 2.85e-03 22_[+1(7.15e-05)]_17 -chr21_37838750_37838800_ 1.90e-02 50 -chr21_45705687_45705737_ 8.63e-04 37_[+1(2.16e-05)]_2 -chr21_45971413_45971463_ 1.95e-04 9_[+1(4.86e-06)]_30 -chr21_45978668_45978718_ 2.59e-04 4_[+1(6.48e-06)]_35 -chr21_45993530_45993580_ 1.95e-04 7_[+1(4.86e-06)]_32 -chr21_46020421_46020471_ 7.78e-04 2_[+1(1.95e-05)]_37 -chr21_46031920_46031970_ 8.89e-05 15_[+1(2.22e-06)]_24 -chr21_46046964_46047014_ 1.80e-05 12_[+1(4.51e-07)]_27 -chr21_46057197_46057247_ 1.95e-04 36_[+1(4.86e-06)]_3 -chr21_46086869_46086919_ 5.54e-03 50 -chr21_46102103_46102153_ 5.54e-03 50 -chr21_47517957_47518007_ 2.59e-04 32_[+1(6.48e-06)]_7 -chr21_47575506_47575556_ 1.22e-03 30_[+1(3.04e-05)]_9 --------------------------------------------------------------------------------- - -******************************************************************************** - - -******************************************************************************** Stopped because requested number of motifs (1) found. -******************************************************************************** - -CPU: ThinkPad-T450s - -********************************************************************************