===============================================
   meme 4.11.2: tests/scripts/test-suite.log
===============================================

# TOTAL: 87
# PASS:  87
# SKIP:  0
# XFAIL: 0
# FAIL:  0
# XPASS: 0
# ERROR: 0

.. contents:: :depth: 2

RUN: ama
========

*******************************************************************************
Test ama1 ...
ama --verbosity 1 --scoring max-odds gomo/motif.meme gomo/seqs.fasta gomo/seqs.bg 1> results/ama1/ama_hlRy2_stdout 2> log
PASSED!
*******************************************************************************
Test ama2 ...
ama --pvalues --verbosity 1 --cs gomo/motif.meme gomo/seqs_red.fasta gomo/seqs.norc.bg 1> results/ama2/ama_7tPUr_stdout 2> log
PASSED!

RUN: ame
========

*******************************************************************************
Test ame1 ...
ame --oc results/ame1 --silent --verbose 1 --bgformat 0 --control common/Klf1-200-100-shuffled.s common/Klf1-200-100.s common/Jaspar-subset.meme &> log
PASSED!

RUN: centrimo
=============

*******************************************************************************
Test centrimo1 ...
centrimo -verbosity 1 -oc results/centrimo -flip common/Klf1.s centrimo/dreme-Klf1.txt &> log
PASSED!

RUN: create_priors
==================

*******************************************************************************
Test create-priors1 ...
create-priors -oc results/create-priors1 create-priors/chrX.fa create-priors/DNaseHS_gm12878.wig &> log
Creating priors with alpha=1.0 and beta=10000
Sequence size is 3000000 bases.
Scores were observed for 4140 bases.
Minimum score is 1
Median score is 1
Maximum score is 3.97638
Sum of scores is 7156.07
Sum of un-normalized priors is 762695
Sum of normalized priors = 10000
Sum of prior distribution = 1
PASSED!
*******************************************************************************
Test create-priors2 ...
create-priors -oc results/create-priors2 create-priors/chrX.fa create-priors/DNaseHS_gm12878.wig &> log
Creating priors with alpha=1.0 and beta=10000
Sequence size is 3000000 bases.
Scores were observed for 4140 bases.
Minimum score is 1
Median score is 1
Maximum score is 3.97638
Sum of scores is 7156.07
Sum of un-normalized priors is 762695
Sum of normalized priors = 10000
Sum of prior distribution = 1
PASSED!

RUN: dreme
==========

*******************************************************************************
Test dreme1 ...
dreme -oc results/dreme1 -v 1 -p common/Klf1-200-100.s &> log
PASSED!
*******************************************************************************
Test dreme2 ...
dreme -norc -oc results/dreme2 -v 1 -p common/Klf1-200-100.s &> log
PASSED!

RUN: fasta-center
=================

*******************************************************************************
Test fasta-center1 ...
fasta-center -len 100 -dna < common/Klf1-200.s 1> results/fasta-center1/fasta-center_UMxYr_stdout 2> log
PASSED!

RUN: fasta-dinucleotide-shuffle
===============================

*******************************************************************************
Test fasta-dinucleotide-shuffle1 ...
fasta-dinucleotide-shuffle -f common/Klf1-200-100.s -t -dinuc 1> results/fasta-dinucleotide-shuffle1/fasta-dinucleotide-shuffle_4hOoV_stdout 2> log
PASSED!

RUN: fimo
=========

*******************************************************************************
Test fimo1 ...
fimo --oc results/fimo1 --motif-pseudo 0.01 fimo/MCM1.meme.html fimo/spiked.fasta &> log
Using motif +1 of width 13.
Using motif -1 of width 13.
Computing q-values.
Estimating pi_0 from a uniformly sampled set of 5308 p-values.
Estimating pi_0.
Estimated pi_0=0.843255
PASSED!
*******************************************************************************
Test fimo2 ...
fimo --oc results/fimo2 --motif 2 --motif 3 --thresh 0.01 common/crp0.meme.html motiph/spiked.fasta &> log
Skipping motif +1.
Skipping motif -1.
Using motif +2 of width 8.
Using motif -2 of width 8.
Computing q-values.
Estimating pi_0 from a uniformly sampled set of 5318 p-values.
Estimating pi_0.
Estimated pi_0=1
Using motif +3 of width 11.
Using motif -3 of width 11.
Computing q-values.
Estimating pi_0 from a uniformly sampled set of 5312 p-values.
Estimating pi_0.
Estimated pi_0=1
PASSED!
*******************************************************************************
Test fimo3 ...
fimo --oc results/fimo3 --psp fimo/GCN4_YPD.psp --prior-dist fimo/prior.dist.txt fimo/GCN4.meme fimo/GCN4_YPD.fasta &> log
Using motif +MA0303.1 of width 21.
Using motif -MA0303.1 of width 21.
Computing q-values.
Estimating pi_0 from a uniformly sampled set of 10000 p-values.
Estimating pi_0.
Estimated pi_0=1
PASSED!
*******************************************************************************
Test fimo4 ...
fimo --oc results/fimo4 --parse-genomic-coord --psp fimo/GCN4_YPD-genomic.psp --prior-dist fimo/prior.dist.txt fimo/GCN4.meme fimo/GCN4_YPD-genomic.fasta &> log
Using motif +MA0303.1 of width 21.
Using motif -MA0303.1 of width 21.
Computing q-values.
Estimating pi_0 from a uniformly sampled set of 10000 p-values.
Estimating pi_0.
Estimated pi_0=1
PASSED!

RUN: glam2
==========

*******************************************************************************
Test glam2_1 ...
glam2 -M -r 3 -n 100 -O results/glam2_1 p common/At.s &> log
The output directory 'results/glam2_1' already exists.
Its contents will be overwritten.
Run 1... 406 iterations
Run 2... 445 iterations
Run 3... 400 iterations

PASSED!

RUN: glam2scan
==============

*******************************************************************************
Test glam2scan1 ...
glam2scan -O results/glam2scan1 p glam2/glam2.txt common/At.s &> log
PASSED!

RUN: gomo
=========

*******************************************************************************
Test gomo1 ...
gomo --seed 1 --nostatus --verbosity 1 --oc results/gomo1 --motifs gomo/motif.meme gomo/GO2Gene.map.csv gomo/ama.nozscoring.xml &> log
PASSED!
*******************************************************************************
Test gomo2 ...
gomo --gs --seed 1 --nostatus --verbosity 1 --oc results/gomo2 --motifs gomo/motif.meme gomo/GO2Gene.map.csv gomo/ama.zscoring.xml gomo/ama.nozscoring.xml &> log
PASSED!

RUN: mast
=========

*******************************************************************************
Test mast1 ...
mast meme/meme.crp0.oops common/crp0.s -oc results/mast1 -nostatus &> log
PASSED!
*******************************************************************************
Test mast2 ...
mast meme/meme.crp0.zoops common/crp0.s -oc results/mast2 -nostatus &> log
PASSED!
*******************************************************************************
Test mast3 ...
mast meme/meme.crp0.tcm common/crp0.s -oc results/mast3 -nostatus &> log
PASSED!
*******************************************************************************
Test mast4 ...
mast meme/meme.INO_up800.oops common/INO_up800.s -oc results/mast4 -nostatus &> log
PASSED!
*******************************************************************************
Test mast5 ...
mast meme/meme.INO_up800.zoops common/INO_up800.s -oc results/mast5 -nostatus &> log
PASSED!
*******************************************************************************
Test mast6 ...
mast meme/meme.INO_up800.tcm common/INO_up800.s -oc results/mast6 -nostatus &> log
PASSED!
*******************************************************************************
Test mast7 ...
mast meme/meme.farntrans5.oops common/farntrans5.s -oc results/mast7 -nostatus &> log
PASSED!
*******************************************************************************
Test mast8 ...
mast meme/meme.farntrans5.zoops common/farntrans5.s -oc results/mast8 -nostatus &> log
PASSED!
*******************************************************************************
Test mast9 ...
mast meme/meme.farntrans5.tcm common/farntrans5.s -oc results/mast9 -nostatus &> log
PASSED!
*******************************************************************************
Test mast10 ...
mast meme/meme.lipocalin.oops common/lipocalin.s -oc results/mast10 -nostatus &> log
PASSED!
*******************************************************************************
Test mast11 ...
mast meme/meme.lipocalin.zoops common/lipocalin.s -oc results/mast11 -nostatus &> log
PASSED!
*******************************************************************************
Test mast12 ...
mast meme/meme.lipocalin.tcm common/lipocalin.s -oc results/mast12 -nostatus &> log
PASSED!
*******************************************************************************
Test mast13 ...
mast meme/meme.adh.oops common/adh.s -oc results/mast13 -nostatus &> log
PASSED!
*******************************************************************************
Test mast14 ...
mast meme/meme.adh.oops - -oc results/mast14 -nostatus -df stdin -dna -seqp < common/mini-drosoph.s &> log
PASSED!
*******************************************************************************
Test mast15 ...
mast meme/meme.adh.zoops common/adh.s -oc results/mast15 -nostatus &> log
PASSED!
*******************************************************************************
Test mast16 ...
mast meme/meme.adh.zoops - -oc results/mast16 -nostatus -df stdin -dna -seqp < common/mini-drosoph.s &> log
PASSED!
*******************************************************************************
Test mast17 ...
mast meme/meme.adh.tcm common/adh.s -oc results/mast17 -nostatus &> log
PASSED!
*******************************************************************************
Test mast18 ...
mast meme/meme.adh.tcm - -oc results/mast18 -nostatus -df stdin -dna -seqp < common/mini-drosoph.s &> log
PASSED!

RUN: mcast
==========

*******************************************************************************
Test mcast1 ...
mcast -oc results/mcast1 meme/meme.lex0.zoops common/lex0.s &> log
Creating HMM from motif array.
Building HMM: (0) 1 2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21 | (22)
Reading sequences in blocks of 434782 characters.
Warning: Cannot estimate pi_0 accurately from fewer than 100 p-values.         total p-values = 14. Using pi_zero = 1.0.
User time for computation: 0.004 seconds
System time for computation: 0 seconds
User time for output: 0.004 seconds
System time for output: 0 seconds
Total user time: 0.008 seconds
Total system time: 0 seconds
PASSED!

RUN: meme
=========

*******************************************************************************
Test meme1 ...
meme common/crp0.s -oc results/meme1 -mod oops -dna -revcomp -nmotifs 2 -minw 8 -nostatus &> log
PASSED!
*******************************************************************************
Test meme2 ...
meme common/crp0.s -oc results/meme2 -mod zoops -dna -revcomp -nmotifs 2 -minw 8 -nostatus &> log
PASSED!
*******************************************************************************
Test meme3 ...
meme common/crp0.s -oc results/meme3 -mod tcm -dna -revcomp -nmotifs 2 -minw 8 -nostatus &> log
PASSED!
*******************************************************************************
Test meme4 ...
meme common/adh.s -oc results/meme4 -mod oops -protein -nmotifs 2 -minw 8 -nostatus &> log
PASSED!
*******************************************************************************
Test meme5 ...
meme common/adh.s -oc results/meme5 -mod zoops -protein -nmotifs 2 -minw 8 -nostatus &> log
PASSED!
*******************************************************************************
Test meme6 ...
meme common/adh.s -oc results/meme6 -mod tcm -protein -nmotifs 2 -minw 8 -nostatus &> log
PASSED!
*******************************************************************************
Test meme_psp ...
meme common/psp_test.s -psp common/psp_test.psp -minsites 5 -dna -revcomp -minw 7 -maxw 12 -nostatus -text 1> results/meme7/meme_n8jYE_stdout 2> log
PASSED!

RUN: motif-in
=============

*******************************************************************************
Generating meme motifs...
meme -oc results/motif.meme.crp0 -nostatus -dna -nmotifs 3 common/crp0.s
*******************************************************************************
Test motif-in.meme.crp0.text ...
meme2images -eps results/motif.meme.crp0/meme.txt results/motif-in.meme.crp0.text
PASSED!
*******************************************************************************
Test motif-in.meme.crp0.xml ...
meme2images -eps results/motif.meme.crp0/meme.xml results/motif-in.meme.crp0.xml
PASSED!
*******************************************************************************
Test motif-in.meme.crp0.html ...
meme2images -eps results/motif.meme.crp0/meme.html results/motif-in.meme.crp0.html
PASSED!
*******************************************************************************
Generating meme motifs...
meme -oc results/motif.meme.lipocalin -nostatus -protein -nmotifs 3 common/lipocalin.s
*******************************************************************************
Test motif-in.meme.lipocalin.text ...
meme2images -eps results/motif.meme.lipocalin/meme.txt results/motif-in.meme.lipocalin.text
PASSED!
*******************************************************************************
Test motif-in.meme.lipocalin.xml ...
meme2images -eps results/motif.meme.lipocalin/meme.xml results/motif-in.meme.lipocalin.xml
PASSED!
*******************************************************************************
Test motif-in.meme.lipocalin.html ...
meme2images -eps results/motif.meme.lipocalin/meme.html results/motif-in.meme.lipocalin.html
PASSED!
*******************************************************************************
Generating meme motifs...
meme -oc results/motif.meme.puf3p -nostatus -rna -nmotifs 3 common/Puf3p-20.s
*******************************************************************************
Test motif-in.meme.puf3p.text ...
meme2images -eps results/motif.meme.puf3p/meme.txt results/motif-in.meme.puf3p.text
PASSED!
*******************************************************************************
Test motif-in.meme.puf3p.xml ...
meme2images -eps results/motif.meme.puf3p/meme.xml results/motif-in.meme.puf3p.xml
PASSED!
*******************************************************************************
Test motif-in.meme.puf3p.html ...
meme2images -eps results/motif.meme.puf3p/meme.html results/motif-in.meme.puf3p.html
PASSED!
*******************************************************************************
Generating meme motifs...
meme -oc results/motif.meme.crp0.extdna -nostatus -alph common/extended_dna.alph -nmotifs 3 common/crp0.s
*******************************************************************************
Test motif-in.meme.crp0.extdna.text ...
meme2images -eps results/motif.meme.crp0.extdna/meme.txt results/motif-in.meme.crp0.extdna.text
PASSED!
*******************************************************************************
Test motif-in.meme.crp0.extdna.xml ...
meme2images -eps results/motif.meme.crp0.extdna/meme.xml results/motif-in.meme.crp0.extdna.xml
PASSED!
*******************************************************************************
Test motif-in.meme.crp0.extdna.html ...
meme2images -eps results/motif.meme.crp0.extdna/meme.html results/motif-in.meme.crp0.extdna.html
PASSED!
*******************************************************************************
Generating dreme motifs...
dreme -oc results/motif.dreme.klf1 -dna -m 3 -p common/Klf1.s
Reading positive sequences common/Klf1.s ...
Shuffling positive sequences...
Looking for motif 1...
Counting positive sequences with each word...
Counting negative sequences with each word...
Applying Fisher's Exact Test to 41938 words...
Generalizing top 100 of 41938 REs to 1 ambiguous characters...
Generalizing top 100 of 686 REs to 2 ambiguous characters...
Generalizing top 61 of 61 REs to 3 ambiguous characters...
Generalizing top 3 of 3 REs to 4 ambiguous characters...
Computing exact p-values for 100 REs...
Best RE was CCMCRCCC GGGYGKGG p-value= 1.8e-071 E-value= 7.6e-067 Unerased_E-value= 7.6e-067
Erasing best word (CCMCRCCC GGGYGKGG)...
Looking for motif 2...
Counting positive sequences with each word...
Counting negative sequences with each word...
Applying Fisher's Exact Test to 41909 words...
Generalizing top 100 of 41909 REs to 1 ambiguous characters...
Generalizing top 100 of 642 REs to 2 ambiguous characters...
Generalizing top 58 of 58 REs to 3 ambiguous characters...
Computing exact p-values for 100 REs...
Best RE was BTTATCW WGATAAV p-value= 5.6e-038 E-value= 2.4e-033 Unerased_E-value= 1.3e-033
Erasing best word (BTTATCW WGATAAV)...
Looking for motif 3...
Counting positive sequences with each word...
Counting negative sequences with each word...
Applying Fisher's Exact Test to 41808 words...
Generalizing top 100 of 41808 REs to 1 ambiguous characters...
Generalizing top 100 of 637 REs to 2 ambiguous characters...
Generalizing top 34 of 34 REs to 3 ambiguous characters...
Computing exact p-values for 100 REs...
Best RE was MCRCCCA TGGGYGK p-value= 6.9e-024 E-value= 2.9e-019 Unerased_E-value= 2.5e-040
Stopping due to hitting the maximum count.
3 motifs with E-value < 0.05 found in 174.0 seconds.
Creating HTML file.
Creating text file.
*******************************************************************************
Test motif-in.dreme.klf1.text ...
meme2images -eps results/motif.dreme.klf1/dreme.txt results/motif-in.dreme.klf1.text
PASSED!
*******************************************************************************
Test motif-in.dreme.klf1.xml ...
meme2images -eps results/motif.dreme.klf1/dreme.xml results/motif-in.dreme.klf1.xml
PASSED!
*******************************************************************************
Test motif-in.dreme.klf1.html ...
meme2images -eps results/motif.dreme.klf1/dreme.html results/motif-in.dreme.klf1.html
PASSED!
*******************************************************************************
Generating dreme motifs...
dreme -oc results/motif.dreme.klf1.extdna -alph common/extended_dna.alph -m 3 -p common/Klf1.s
Reading positive sequences common/Klf1.s ...
Shuffling positive sequences...
Looking for motif 1...
Counting positive sequences with each word...
Counting negative sequences with each word...
Applying Fisher's Exact Test to 41938 words...
Generalizing top 100 of 41938 REs to 1 ambiguous characters...
Generalizing top 100 of 695 REs to 2 ambiguous characters...
Generalizing top 62 of 62 REs to 3 ambiguous characters...
Generalizing top 3 of 3 REs to 4 ambiguous characters...
Computing exact p-values for 100 REs...
Best RE was CCMCRCCC GGGYGKGG p-value= 1.8e-071 E-value= 7.6e-067 Unerased_E-value= 7.6e-067
Erasing best word (CCMCRCCC GGGYGKGG)...
Looking for motif 2...
Counting positive sequences with each word...
Counting negative sequences with each word...
Applying Fisher's Exact Test to 41909 words...
Generalizing top 100 of 41909 REs to 1 ambiguous characters...
Generalizing top 100 of 650 REs to 2 ambiguous characters...
Generalizing top 57 of 57 REs to 3 ambiguous characters...
Computing exact p-values for 100 REs...
Best RE was BTTATCW WGATAAV p-value= 5.6e-038 E-value= 2.4e-033 Unerased_E-value= 1.3e-033
Erasing best word (BTTATCW WGATAAV)...
Looking for motif 3...
Counting positive sequences with each word...
Counting negative sequences with each word...
Applying Fisher's Exact Test to 41808 words...
Generalizing top 100 of 41808 REs to 1 ambiguous characters...
Generalizing top 100 of 644 REs to 2 ambiguous characters...
Generalizing top 32 of 32 REs to 3 ambiguous characters...
Computing exact p-values for 100 REs...
Best RE was MCRCCCA TGGGYGK p-value= 6.9e-024 E-value= 2.9e-019 Unerased_E-value= 2.5e-040
Stopping due to hitting the maximum count.
3 motifs with E-value < 0.05 found in 259.6 seconds.
Creating HTML file.
Creating text file.
*******************************************************************************
Test motif-in.dreme.klf1.extdna.text ...
meme2images -eps results/motif.dreme.klf1.extdna/dreme.txt results/motif-in.dreme.klf1.extdna.text
PASSED!
*******************************************************************************
Test motif-in.dreme.klf1.extdna.xml ...
meme2images -eps results/motif.dreme.klf1.extdna/dreme.xml results/motif-in.dreme.klf1.extdna.xml
PASSED!
*******************************************************************************
Test motif-in.dreme.klf1.extdna.html ...
meme2images -eps results/motif.dreme.klf1.extdna/dreme.html results/motif-in.dreme.klf1.extdna.html
PASSED!
*******************************************************************************
Generating dreme motifs...
dreme -oc results/motif.dreme.puf3p -rna -m 3 -p common/Puf3p.s
Reading positive sequences common/Puf3p.s ...
Shuffling positive sequences...
Looking for motif 1...
Counting positive sequences with each word...
Counting negative sequences with each word...
Applying Fisher's Exact Test to 58954 words...
Generalizing top 100 of 58954 REs to 1 ambiguous characters...
Generalizing top 100 of 499 REs to 2 ambiguous characters...
Generalizing top 35 of 35 REs to 3 ambiguous characters...
Computing exact p-values for 100 REs...
Best RE was UGUAHAUA p-value= 2.1e-068 E-value= 1.2e-063 Unerased_E-value= 1.2e-063
Erasing best word (UGUAHAUA)...
Looking for motif 2...
Counting positive sequences with each word...
Counting negative sequences with each word...
Applying Fisher's Exact Test to 58665 words...
Generalizing top 100 of 58665 REs to 1 ambiguous characters...
Generalizing top 100 of 270 REs to 2 ambiguous characters...
Generalizing top 14 of 14 REs to 3 ambiguous characters...
Computing exact p-values for 100 REs...
Best RE was YAUAUAWA p-value= 2.3e-019 E-value= 1.3e-014 Unerased_E-value= 1.7e-020
Erasing best word (YAUAUAWA)...
Looking for motif 3...
Counting positive sequences with each word...
Counting negative sequences with each word...
Applying Fisher's Exact Test to 58552 words...
Generalizing top 100 of 58552 REs to 1 ambiguous characters...
Generalizing top 100 of 201 REs to 2 ambiguous characters...
Generalizing top 24 of 24 REs to 3 ambiguous characters...
Computing exact p-values for 100 REs...
Best RE was GAARR p-value= 1.1e-014 E-value= 6.2e-010 Unerased_E-value= 6.2e-010
Stopping due to hitting the maximum count.
3 motifs with E-value < 0.05 found in 36.2 seconds.
Creating HTML file.
Creating text file.
*******************************************************************************
Test motif-in.dreme.puf3p.text ...
meme2images -eps results/motif.dreme.puf3p/dreme.txt results/motif-in.dreme.puf3p.text
PASSED!
*******************************************************************************
Test motif-in.dreme.puf3p.xml ...
meme2images -eps results/motif.dreme.puf3p/dreme.xml results/motif-in.dreme.puf3p.xml
PASSED!
*******************************************************************************
Test motif-in.dreme.puf3p.html ...
meme2images -eps results/motif.dreme.puf3p/dreme.html results/motif-in.dreme.puf3p.html
PASSED!

RUN: motiph
===========

*******************************************************************************
Test motiph1 ...
motiph --seed 0 --bg 2 --pseudocount 0.01 --oc results/motiph1 motiph/spiked.aln motiph/yeast.tree motiph/MCM1.meme.html &> log
Using motif +1 of width 13.
Read alignment from motiph/spiked.aln.
Trimmed tree: (Sbay:0.33300,(Smik:0.21600,(Spar:0.10500,Scer:0.14600):0.07700):0.08600);
Computing q-values.
Estimating pi_0 from all 879 observed p-values.
Estimating pi_0.
Estimated pi_0=0.859743
Using motif -1 of width 13.
Read alignment from motiph/spiked.aln.
Trimmed tree: (Sbay:0.33300,(Smik:0.21600,(Spar:0.10500,Scer:0.14600):0.07700):0.08600);
Computing q-values.
Estimating pi_0 from all 879 observed p-values.
Estimating pi_0.
Estimated pi_0=0.813862
Total number of positions scored: 1758
PASSED!
*******************************************************************************
Test motiph2 ...
motiph --seed 0 --bg 2 --pseudocount 0.01 --oc results/motiph2 --output-pthresh 1 --motif 2 --motif 3 motiph/spiked.aln motiph/yeast.tree common/crp0.meme.html &> log
Using motif +2 of width 8.
Read alignment from motiph/spiked.aln.
Trimmed tree: (Sbay:0.33300,(Smik:0.21600,(Spar:0.10500,Scer:0.14600):0.07700):0.08600);
Computing q-values.
Estimating pi_0 from all 1243 observed p-values.
Estimating pi_0.
Estimated pi_0=1
Using motif -2 of width 8.
Read alignment from motiph/spiked.aln.
Trimmed tree: (Sbay:0.33300,(Smik:0.21600,(Spar:0.10500,Scer:0.14600):0.07700):0.08600);
Computing q-values.
Estimating pi_0 from all 1243 observed p-values.
Estimating pi_0.
Estimated pi_0=1
Using motif +3 of width 11.
Read alignment from motiph/spiked.aln.
Trimmed tree: (Sbay:0.33300,(Smik:0.21600,(Spar:0.10500,Scer:0.14600):0.07700):0.08600);
Computing q-values.
Estimating pi_0 from all 1014 observed p-values.
Estimating pi_0.
Estimated pi_0=1
Using motif -3 of width 11.
Read alignment from motiph/spiked.aln.
Trimmed tree: (Sbay:0.33300,(Smik:0.21600,(Spar:0.10500,Scer:0.14600):0.07700):0.08600);
Computing q-values.
Estimating pi_0 from all 1014 observed p-values.
Estimating pi_0.
Estimated pi_0=1
Total number of positions scored: 4514
PASSED!

RUN: pspgen
===========

*******************************************************************************
Test psp-gen1 ...
psp-gen -revcomp -pos psp-gen/one-peak-dna.fasta -neg psp-gen/all-A.fasta 1> results/pspgen1/psp-gen_BtEjc_stdout 2> log
PASSED!
*******************************************************************************
Test psp-gen2 ...
psp-gen -protein -maxrange -triples -pos psp-gen/one-peak-protein.fasta -neg psp-gen/all-A.fasta 1> results/pspgen2/psp-gen_bEP2v_stdout 2> log
PASSED!
*******************************************************************************
Test psp-gen3 ...
psp-gen -alph common/extended_dna.alph -revcomp -pos psp-gen/one-peak-dna.fasta -neg psp-gen/all-A.fasta 1> results/pspgen1/psp-gen_OZx64_stdout 2> log
PASSED!

RUN: qvalue
===========

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Test qvalue1 ...
qvalue --header 1 --append --column 2 --seed 7718 qvalue/uniform.txt 1> results/qvalue1/qvalue_awzV__stdout 2> log
Read 1000 values from qvalue/uniform.txt.
PASSED!

RUN: spamo
==========

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Test spamo1 ...
spamo -oc results/spamo1 -verbosity 1 -margin 20 -shared 1 spamo/limits.fasta spamo/primary.meme spamo/secondary.meme &> log
PASSED!
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Test spamo2 ...
spamo -oc results/spamo2 -verbosity 1 -margin 20 -shared 1 spamo/random.fasta spamo/primary.meme spamo/secondary.meme &> log
PASSED!

RUN: tomtom
===========

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Test tomtom_allr ...
tomtom -verbosity 1 -dist allr -oc results/tomtom1 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: Target database size too small (5). Provide at least 50 motifs for accurate p-value computation
PASSED!
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Test tomtom_ed ...
tomtom -verbosity 1 -dist ed -oc results/tomtom2 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: Target database size too small (5). Provide at least 50 motifs for accurate p-value computation
PASSED!
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Test tomtom_kullback ...
tomtom -verbosity 1 -dist kullback -oc results/tomtom3 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: Target database size too small (5). Provide at least 50 motifs for accurate p-value computation
PASSED!
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Test tomtom_pearson ...
tomtom -verbosity 1 -dist pearson -oc results/tomtom4 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: Target database size too small (5). Provide at least 50 motifs for accurate p-value computation
PASSED!
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Test tomtom_sandelin ...
tomtom -verbosity 1 -dist sandelin -oc results/tomtom5 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: Target database size too small (5). Provide at least 50 motifs for accurate p-value computation
PASSED!
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Test tomtom_blic1 ...
tomtom -verbosity 1 -dist blic1 -oc results/tomtom6 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: Target database size too small (5). Provide at least 50 motifs for accurate p-value computation
PASSED!
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Test tomtom_blic5 ...
tomtom -verbosity 1 -dist blic5 -oc results/tomtom7 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: Target database size too small (5). Provide at least 50 motifs for accurate p-value computation
PASSED!
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Test tomtom_allr_cs ...
tomtom -verbosity 1 -dist allr -oc results/tomtom8 common/sample.meme common/sample.meme &> log
Warning: Target database size too small (5). Provide at least 50 motifs for accurate p-value computation
PASSED!
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Test tomtom_ed_cs ...
tomtom -verbosity 1 -dist ed -oc results/tomtom9 common/sample.meme common/sample.meme &> log
Warning: Target database size too small (5). Provide at least 50 motifs for accurate p-value computation
PASSED!
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Test tomtom_kullback_cs ...
tomtom -verbosity 1 -dist kullback -oc results/tomtom10 common/sample.meme common/sample.meme &> log
Warning: Target database size too small (5). Provide at least 50 motifs for accurate p-value computation
PASSED!
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Test tomtom_pearson_cs ...
tomtom -verbosity 1 -dist pearson -oc results/tomtom11 common/sample.meme common/sample.meme &> log
Warning: Target database size too small (5). Provide at least 50 motifs for accurate p-value computation
PASSED!
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Test tomtom_sandelin_cs ...
tomtom -verbosity 1 -dist sandelin -oc results/tomtom12 common/sample.meme common/sample.meme &> log
Warning: Target database size too small (5). Provide at least 50 motifs for accurate p-value computation
PASSED!
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Test tomtom_blic1_cs ...
tomtom -verbosity 1 -dist blic1 -oc results/tomtom13 common/sample.meme common/sample.meme &> log
Warning: Target database size too small (5). Provide at least 50 motifs for accurate p-value computation
PASSED!
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Test tomtom_blic5_cs ...
tomtom -verbosity 1 -dist blic5 -oc results/tomtom14 common/sample.meme common/sample.meme &> log
Warning: Target database size too small (5). Provide at least 50 motifs for accurate p-value computation
PASSED!