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===============================================

meme 4.12.0: tests/scripts/test-suite.log


===============================================

# TOTAL: 108
# PASS: 71
# SKIP: 12
# XFAIL: 0
# FAIL: 25
# XPASS: 0
# ERROR: 0

.. contents:: :depth: 2

RUN: ama
========

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

RUN: ame
========

*******************************************************************************
Test ame1 ...
ame --oc results/ame1 --silent --verbose 1 --bgformat 0 --xalph
common/alphabet_rna.txt --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.xml &> 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 -n common/Klf1-200-100-
shuffled.s &> log
PASSED!
*******************************************************************************
Test dreme2 ...
dreme -norc -oc results/dreme2 -v 1 -p common/Klf1-200-100.s -n common/Klf1-200-
100-shuffled.s &> log
PASSED!
*******************************************************************************
Test dreme3 ...
dreme-py3 -oc results/dreme3 -v 1 -p common/Klf1-200-100.s -n common/Klf1-200-100-
shuffled.s &> log
PASSED!
*******************************************************************************
Test dreme4 ...
dreme-py3 -norc -oc results/dreme4 -v 1 -p common/Klf1-200-100.s -n common/Klf1-
200-100-shuffled.s &> log
PASSED!

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

*******************************************************************************
Test fasta-center1 ...
fasta-center -len 100 -dna < common/Klf1-200.s 1> results/fasta-center1/fasta-
center_eexA7_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_TjmZp_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 +TTTCCYDWTTBGGAAATW of width 18.
Using motif -TTTCCYDWTTBGGAAATW of width 18.
Computing q-values.
Estimating pi_0 from a uniformly sampled set of 5298 p-values.
Estimating pi_0.
Estimated pi_0=0.798732
PASSED!
*******************************************************************************
Test fimo2 ...
fimo --oc results/fimo2 --motif CGGYGGGG --motif GCATCRGRBSAGA --no-qvalue --thresh
0.01 common/crp0.meme.xml motiph/spiked.fasta &> log
Skipping motif +TKTGANCNABNTCACAHWT.
Skipping motif -TKTGANCNABNTCACAHWT.
Using motif +CGGYGGGG of width 8.
Using motif -CGGYGGGG of width 8.
Using motif +GCATCRGRBSAGA of width 13.
Using motif -GCATCRGRBSAGA of width 13.
PASSED!
*******************************************************************************
Test fimo3 ...
fimo --oc results/fimo3 --psp fimo/GCN4_YPD.psp --prior-dist fimo/prior.dist.txt
fimo/GCN4.meme.txt 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.txt 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.txt 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.txt gomo/GO2Gene.map.csv gomo/ama.zscoring.xml
gomo/ama.nozscoring.xml &> log
PASSED!

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

*******************************************************************************
Test mast1 ...
mast meme/meme.crp0.oops.txt common/crp0.s -oc results/mast1 -nostatus &> log
PASSED!
*******************************************************************************
Test mast2 ...
mast meme/meme.crp0.zoops.txt common/crp0.s -oc results/mast2 -nostatus &> log
PASSED!
*******************************************************************************
Test mast3 ...
mast meme/meme.crp0.tcm.txt common/crp0.s -oc results/mast3 -nostatus &> log
PASSED!
*******************************************************************************
Test mast4 ...
mast meme/meme.INO_up800.oops.txt common/INO_up800.s -oc results/mast4 -nostatus &>
log
PASSED!
*******************************************************************************
Test mast5 ...
mast meme/meme.INO_up800.zoops.txt common/INO_up800.s -oc results/mast5 -nostatus
&> log
PASSED!
*******************************************************************************
Test mast6 ...
mast meme/meme.INO_up800.tcm.txt common/INO_up800.s -oc results/mast6 -nostatus &>
log
PASSED!
*******************************************************************************
Test mast7 ...
mast meme/meme.farntrans5.oops.txt common/farntrans5.s -oc results/mast7 -nostatus
&> log
PASSED!
*******************************************************************************
Test mast8 ...
mast meme/meme.farntrans5.zoops.txt common/farntrans5.s -oc results/mast8 -nostatus
&> log
PASSED!
*******************************************************************************
Test mast9 ...
mast meme/meme.farntrans5.tcm.txt common/farntrans5.s -oc results/mast9 -nostatus
&> log
PASSED!
*******************************************************************************
Test mast10 ...
mast meme/meme.lipocalin.oops.txt common/lipocalin.s -oc results/mast10 -nostatus
&> log
PASSED!
*******************************************************************************
Test mast11 ...
mast meme/meme.lipocalin.zoops.txt common/lipocalin.s -oc results/mast11 -nostatus
&> log
PASSED!
*******************************************************************************
Test mast12 ...
mast meme/meme.lipocalin.tcm.txt common/lipocalin.s -oc results/mast12 -nostatus &>
log
PASSED!
*******************************************************************************
Test mast13 ...
mast meme/meme.adh.oops.txt common/adh.s -oc results/mast13 -nostatus &> log
PASSED!
*******************************************************************************
Test mast14 ...
mast meme/meme.adh.oops.txt - -oc results/mast14 -nostatus -df stdin -dna -seqp <
common/mini-drosoph.s &> log
PASSED!
*******************************************************************************
Test mast15 ...
mast meme/meme.adh.zoops.txt common/adh.s -oc results/mast15 -nostatus &> log
PASSED!
*******************************************************************************
Test mast16 ...
mast meme/meme.adh.zoops.txt - -oc results/mast16 -nostatus -df stdin -dna -seqp <
common/mini-drosoph.s &> log
PASSED!
*******************************************************************************
Test mast17 ...
mast meme/meme.adh.tcm.txt common/adh.s -oc results/mast17 -nostatus &> log
PASSED!
*******************************************************************************
Test mast18 ...
mast meme/meme.adh.tcm.txt - -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.txt 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 seconds
System time for computation: 0 seconds
User time for output: 0 seconds
System time for output: 0 seconds
Total user time: 0 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
-------------------------------------------------------------------------------
meme exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test meme2 ...
meme common/crp0.s -oc results/meme2 -mod zoops -dna -revcomp -nmotifs 2 -minw 8
-nostatus &> log
-------------------------------------------------------------------------------
meme exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test meme3 ...
meme common/crp0.s -oc results/meme3 -mod tcm -dna -revcomp -nmotifs 2 -minw 8
-nostatus &> log
-------------------------------------------------------------------------------
meme exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test meme4 ...
meme common/adh.s -oc results/meme4 -mod oops -protein -nmotifs 2 -minw 8 -nostatus
&> log
-------------------------------------------------------------------------------
meme exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test meme5 ...
meme common/adh.s -oc results/meme5 -mod zoops -protein -nmotifs 2 -minw 8
-nostatus &> log
-------------------------------------------------------------------------------
meme exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test meme6 ...
meme common/adh.s -oc results/meme6 -mod tcm -protein -nmotifs 2 -minw 8 -nostatus
&> log
-------------------------------------------------------------------------------
meme exited with value 127 indicating failure.
FAILED!
*******************************************************************************
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_iAFsk_stdout 2> log
-------------------------------------------------------------------------------
meme exited with value 127 indicating failure.
FAILED!

RUN: meme-chip
==============

*******************************************************************************
Test meme-chip1 ...
meme-chip -oc results/meme-chip1 -db meme-chip/JASPAR_CORE_2014_vertebrates.meme
meme-chip/Klf1.100.s &> log
Starting getsize: getsize results/meme-chip1/Klf1.100.s 1> $metrics
getsize ran successfully in 0.044691 seconds
Starting fasta-most: fasta-most -min 50 < results/meme-chip1/Klf1.100.s 1> $metrics
fasta-most ran successfully in 0.106275 seconds
Starting fasta-center: fasta-center -dna -len 100 < results/meme-chip1/Klf1.100.s
1> results/meme-chip1/seqs-centered
fasta-center ran successfully in 0.110034 seconds
Starting fasta-shuffle-letters: fasta-shuffle-letters results/meme-chip1/seqs-
centered results/meme-chip1/seqs-shuffled -kmer 2 -tag -dinuc -dna -seed 1
fasta-shuffle-letters ran successfully in 0.061528 seconds
Starting fasta-get-markov: fasta-get-markov -nostatus -nosummary -dna -m 1
results/meme-chip1/Klf1.100.s results/meme-chip1/background
fasta-get-markov ran successfully in 0.044524 seconds
Starting meme: meme results/meme-chip1/seqs-centered -oc results/meme-
chip1/meme_out -mod zoops -nmotifs 3 -minw 6 -maxw 30 -bfile results/meme-
chip1/background -dna -revcomp -nostatus
meme exited with error code 127
Starting dreme: dreme -v 1 -oc results/meme-chip1/dreme_out -png -dna -p
results/meme-chip1/seqs-centered -n results/meme-chip1/seqs-shuffled
dreme ran successfully in 1.787832 seconds
Starting centrimo: centrimo -seqlen 500 -verbosity 1 -oc results/meme-
chip1/centrimo_out -bfile results/meme-chip1/background results/meme-
chip1/Klf1.100.s results/meme-chip1/dreme_out/dreme.xml meme-
chip/JASPAR_CORE_2014_vertebrates.meme
centrimo ran successfully in 0.990455 seconds
Starting tomtom: tomtom -verbosity 1 -oc results/meme-chip1/dreme_tomtom_out -min-
overlap 5 -dist pearson -evalue -thresh 1 -no-ssc -bfile results/meme-
chip1/background results/meme-chip1/dreme_out/dreme.xml meme-
chip/JASPAR_CORE_2014_vertebrates.meme
tomtom ran successfully in 0.799286 seconds
Starting tomtom: tomtom -verbosity 1 -text -thresh 0.1 results/meme-
chip1/combined.meme results/meme-chip1/combined.meme 1> results/meme-
chip1/motif_alignment.txt
tomtom ran successfully in 0.153025 seconds
Starting spamo: spamo -verbosity 1 -oc results/meme-chip1/spamo_out_1 -bgfile
results/meme-chip1/background -primary CACRCCC results/meme-chip1/Klf1.100.s
results/meme-chip1/dreme_out/dreme.xml results/meme-chip1/dreme_out/dreme.xml meme-
chip/JASPAR_CORE_2014_vertebrates.meme
spamo ran successfully in 1.450754 seconds
Starting spamo: spamo -verbosity 1 -oc results/meme-chip1/spamo_out_2 -bgfile
results/meme-chip1/background -primary MA0140.2 results/meme-chip1/Klf1.100.s meme-
chip/JASPAR_CORE_2014_vertebrates.meme results/meme-chip1/dreme_out/dreme.xml meme-
chip/JASPAR_CORE_2014_vertebrates.meme
spamo ran successfully in 2.04374 seconds
Starting fimo: fimo --parse-genomic-coord --verbosity 1 --oc results/meme-
chip1/fimo_out_1 --bgfile results/meme-chip1/background --motif CACRCCC
results/meme-chip1/dreme_out/dreme.xml results/meme-chip1/Klf1.100.s
fimo ran successfully in 0.138265 seconds
Starting fimo: fimo --parse-genomic-coord --verbosity 1 --oc results/meme-
chip1/fimo_out_2 --bgfile results/meme-chip1/background --motif MA0140.2 meme-
chip/JASPAR_CORE_2014_vertebrates.meme results/meme-chip1/Klf1.100.s
fimo ran successfully in 0.669449 seconds
Starting meme-chip_html_to_tsv: meme-chip_html_to_tsv results/meme-chip1/meme-
chip.html results/meme-chip1/summary.tsv
meme-chip_html_to_tsv ran successfully in 0.189308 seconds
-------------------------------------------------------------------------------
A difference was detected between the reference and tested json files.
Got data:programs@6:status=0 but expected data:programs@6:status=32512.
2,11c2,9
< 1 MEME WGGGYGTGGY MEME-1 WGGGYGTGGY 10 29 1.6e-012 MEME meme-
chip/JASPAR_CORE_2014_vertebrates.meme MA0493.1 (Klf1)
http://jaspar2014.genereg.net?ID=MA0493.1&rm=present&collection=CORE
< 2 meme-chip/JASPAR_CORE_2014_vertebrates.meme MA0039.2 Klf4 DGGGYGKGGC
10 81 1.9e-006 CENTRIMO
http://jaspar2014.genereg.net?ID=MA0039.2&rm=present&collection=CORE
< 3 DREME CACRCCC DREME-1 CACRCCC 7 27 1.9e-006 DREME meme-
chip/JASPAR_CORE_2014_vertebrates.meme MA0493.1 (Klf1)
http://jaspar2014.genereg.net?ID=MA0493.1&rm=present&collection=CORE
< 4 meme-chip/JASPAR_CORE_2014_vertebrates.meme MA0493.1 Klf1 RRCCACACCCW
11 70 6.7e-006 CENTRIMO
http://jaspar2014.genereg.net?ID=MA0493.1&rm=present&collection=CORE
< 5 meme-chip/JASPAR_CORE_2014_vertebrates.meme MA0599.1 KLF5 GCCCCDCCCH
10 74 6.9e-005 CENTRIMO
http://jaspar2014.genereg.net?ID=MA0599.1&rm=present&collection=CORE
< 6 MEME WGCYYCHBCCCTCYC MEME-2 WGCYYCHBCCCTCYC 15 30 6.4e-003
MEME meme-chip/JASPAR_CORE_2014_vertebrates.meme MA0471.1 (E2F6)
http://jaspar2014.genereg.net?ID=MA0471.1&rm=present&collection=CORE
< 7 meme-chip/JASPAR_CORE_2014_vertebrates.meme MA0140.2 TAL1::GATA1
MTTATCWSNNNNNHVCAG 18 50 1.9e-002 CENTRIMO
http://jaspar2014.genereg.net?ID=MA0140.2&rm=present&collection=CORE
< 8 meme-chip/JASPAR_CORE_2014_vertebrates.meme MA0079.3 SP1 GCCCCKCCCCC
11 56 2.1e-002 CENTRIMO
http://jaspar2014.genereg.net?ID=MA0079.3&rm=present&collection=CORE
< 9 meme-chip/JASPAR_CORE_2014_vertebrates.meme MA0035.3 Gata1 TYCTTATCTSY
11 56 2.9e-002 CENTRIMO
http://jaspar2014.genereg.net?ID=MA0035.3&rm=present&collection=CORE
< 10 meme-chip/JASPAR_CORE_2014_vertebrates.meme MA0036.2 GATA2
WRDTTCTTATCTSH 14 58 3.3e-002 CENTRIMO
http://jaspar2014.genereg.net?ID=MA0036.2&rm=present&collection=CORE
---
> 1 meme-chip/JASPAR_CORE_2014_vertebrates.meme MA0039.2 Klf4 DGGGYGKGGC
10 81 1.9e-006 CENTRIMO
http://jaspar2014.genereg.net?ID=MA0039.2&rm=present&collection=CORE
> 2 DREME CACRCCC DREME-1 CACRCCC 7 27 1.9e-006 DREME meme-
chip/JASPAR_CORE_2014_vertebrates.meme MA0493.1 (Klf1)
http://jaspar2014.genereg.net?ID=MA0493.1&rm=present&collection=CORE
> 3 meme-chip/JASPAR_CORE_2014_vertebrates.meme MA0493.1 Klf1 RRCCACACCCW
11 70 6.6e-006 CENTRIMO
http://jaspar2014.genereg.net?ID=MA0493.1&rm=present&collection=CORE
> 4 meme-chip/JASPAR_CORE_2014_vertebrates.meme MA0599.1 KLF5 GCCCCDCCCH
10 74 6.8e-005 CENTRIMO
http://jaspar2014.genereg.net?ID=MA0599.1&rm=present&collection=CORE
> 5 meme-chip/JASPAR_CORE_2014_vertebrates.meme MA0140.2 TAL1::GATA1
MTTATCWSNNNNNHVCAG 18 50 1.8e-002 CENTRIMO
http://jaspar2014.genereg.net?ID=MA0140.2&rm=present&collection=CORE
> 6 meme-chip/JASPAR_CORE_2014_vertebrates.meme MA0079.3 SP1 GCCCCKCCCCC
11 56 2.0e-002 CENTRIMO
http://jaspar2014.genereg.net?ID=MA0079.3&rm=present&collection=CORE
> 7 meme-chip/JASPAR_CORE_2014_vertebrates.meme MA0035.3 Gata1 TYCTTATCTSY
11 56 2.8e-002 CENTRIMO
http://jaspar2014.genereg.net?ID=MA0035.3&rm=present&collection=CORE
> 8 meme-chip/JASPAR_CORE_2014_vertebrates.meme MA0036.2 GATA2
WRDTTCTTATCTSH 14 58 3.2e-002 CENTRIMO
http://jaspar2014.genereg.net?ID=MA0036.2&rm=present&collection=CORE
10,24c10
< MOTIF 1 WGGGYGTGGY-MEME-1
<
< letter-probability matrix: alength= 4 w= 10 nsites= 29 E= 1.6e-012
< 0.448276 0.034483 0.000000 0.517241
< 0.034483 0.000000 0.965517 0.000000
< 0.000000 0.000000 1.000000 0.000000
< 0.000000 0.000000 0.965517 0.034483
< 0.000000 0.344828 0.000000 0.655172
< 0.000000 0.000000 1.000000 0.000000
< 0.034483 0.034483 0.068966 0.862069
< 0.000000 0.034483 0.965517 0.000000
< 0.000000 0.103448 0.758621 0.137931
< 0.068966 0.586207 0.034483 0.310345
<
< MOTIF 2 MA0039.2-Klf4
---
> MOTIF 1 MA0039.2-Klf4
38c24
< MOTIF 3 CACRCCC-DREME-1
---
> MOTIF 2 CACRCCC-DREME-1
49c35
< MOTIF 4 MA0493.1-Klf1
---
> MOTIF 3 MA0493.1-Klf1
64c50
< MOTIF 5 MA0599.1-KLF5
---
> MOTIF 4 MA0599.1-KLF5
78,97c64
< MOTIF 6 WGCYYCHBCCCTCYC-MEME-2
<
< letter-probability matrix: alength= 4 w= 15 nsites= 30 E= 1.2e+002
< 0.433333 0.000000 0.166667 0.400000
< 0.133333 0.133333 0.700000 0.033333
< 0.100000 0.733333 0.000000 0.166667
< 0.166667 0.400000 0.033333 0.400000
< 0.100000 0.533333 0.033333 0.333333
< 0.100000 0.833333 0.000000 0.066667
< 0.300000 0.266667 0.100000 0.333333
< 0.000000 0.333333 0.266667 0.400000
< 0.000000 1.000000 0.000000 0.000000
< 0.000000 0.866667 0.000000 0.133333
< 0.100000 0.666667 0.000000 0.233333
< 0.033333 0.000000 0.066667 0.900000
< 0.200000 0.566667 0.233333 0.000000
< 0.033333 0.566667 0.000000 0.400000
< 0.033333 0.933333 0.000000 0.033333
<
< MOTIF 7 MA0140.2-TAL1::GATA1
---
> MOTIF 5 MA0140.2-TAL1::GATA1
119c86
< MOTIF 8 MA0079.3-SP1
---
> MOTIF 6 MA0079.3-SP1
134c101
< MOTIF 9 MA0035.3-Gata1
---
> MOTIF 7 MA0035.3-Gata1
149c116
< MOTIF 10 MA0036.2-GATA2
---
> MOTIF 8 MA0036.2-GATA2
FAILED!

RUN: momo
=========

*******************************************************************************
Test momo1 ...
momo simple --oc results/momo1 momo/small-tide-mod.txt &> log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test momo2 ...
momo simple --oc results/momo2 --protein-database momo/small-yeast.fasta
momo/small-tide-mod.txt &> log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test momo3 ...
momo simple --oc results/momo3 --single-motif-per-mass T momo/small-tide-mod.txt &>
log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test momo4 ...
momo simple --oc results/momo4 --protein-database momo/small-yeast.fasta --hash-
fasta 0 momo/small-tide-mod.txt &> log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test momo5 ...
momo simple --oc results/momo5 --eliminate-repeats 3 momo/small-tide-mod.txt &> log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test momo6 ...
momo simple --oc results/momo6 --eliminate-repeats 0 momo/small-tide-mod.txt &> log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test momo7 ...
momo simple --oc results/momo7 --filter "xcorr rank,le,3" momo/small-tide-mod.txt
&> log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test momo8 ...
momo simple --oc results/momo8 --fg-filetype prealigned momo/small-tide-mod-
phospho.txt &> log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test momo9 ...
momo simple --oc results/momo9 --fg-filetype fasta momo/small-tide-mod-
phospho.fasta &> log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test momo10 ...
momo simple --oc results/momo10 momo/small-tide-mod-1-out-of-2.txt momo/small-tide-
mod-2-out-of-2.txt &> log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test momo11 ...
momo motifx --oc results/momo11 --protein-database momo/small-yeast.fasta --score-
threshold 0.05 --count-threshold 1 momo/small-tide-mod.txt &> log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test momo12 ...
momo motifx --oc results/momo12 --protein-database momo/small-yeast.fasta --score-
threshold 0.05 --count-threshold 1 --single-motif-per-mass T momo/small-tide-
mod.txt &> log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test momo13 ...
momo motifx --oc results/momo13 --protein-database momo/small-yeast.fasta --score-
threshold 0.05 --count-threshold 1 --fg-filetype prealigned momo/small-tide-mod-
phospho.txt &> log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test momo14 ...
momo motifx --oc results/momo14 --protein-database momo/small-yeast-prealigned-no-
unknowns.txt --score-threshold 0.05 --count-threshold 1 --fg-filetype prealigned
--bg-filetype prealigned momo/small-tide-mod-phospho.txt &> log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test momo15 ...
momo simple --oc results/momo15 --sequence-column Peptide momo/small-msgf-mod.txt
&> log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test momo16 ...
momo simple --oc results/momo16 --sequence-column "modified sequence" momo/small-
comet-mod.txt &> log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!
*******************************************************************************
Test momo17 ...
momo modl --oc results/momo17 --protein-database momo/small-yeast.fasta momo/small-
tide-mod.txt &> log
-------------------------------------------------------------------------------
momo exited with value 127 indicating failure.
FAILED!

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 ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.crp0.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.crp0.html ...
SKIPPED!
*******************************************************************************
Generating meme motifs...
meme -oc results/motif.meme.lipocalin -nostatus -protein -nmotifs 3
common/lipocalin.s
*******************************************************************************
Test motif-in.meme.lipocalin.text ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.lipocalin.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.lipocalin.html ...
SKIPPED!
*******************************************************************************
Generating meme motifs...
meme -oc results/motif.meme.puf3p -nostatus -rna -nmotifs 3 common/Puf3p-20.s
*******************************************************************************
Test motif-in.meme.puf3p.text ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.puf3p.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.puf3p.html ...
SKIPPED!
*******************************************************************************
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 ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.crp0.extdna.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.crp0.extdna.html ...
SKIPPED!
*******************************************************************************
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 88.6 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 135.6 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 15.7 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 CGGYGGGG --motif GCATCRGRBSAGA motiph/spiked.aln motiph/yeast.tree
common/crp0.meme.html &> log
Using motif +CGGYGGGG 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 -CGGYGGGG 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 +GCATCRGRBSAGA 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=0.976836
Using motif -GCATCRGRBSAGA 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=0.993591
Total number of positions scored: 4244
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_fZWg1_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_Knyim_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_ZOxdR_stdout 2> log
PASSED!

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

*******************************************************************************
Test qvalue1 ...
qvalue --header 1 --append --column 2 --seed 7718 qvalue/uniform.txt 1>
results/qvalue1/qvalue_OFSiO_stdout 2> log
Read 1000 values from qvalue/uniform.txt.
PASSED!
*******************************************************************************
Test qvalue2 ...
qvalue --null qvalue/null.txt qvalue/observed.txt 1>
results/qvalue2/qvalue_BqDF__stdout 2> log
Read 5 values from qvalue/observed.txt.
Read 10 values from qvalue/null.txt.
Converting scores to p-values.
PASSED!
RUN: spamo
==========

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

*******************************************************************************
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!
*******************************************************************************
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!
*******************************************************************************
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!
*******************************************************************************
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!
*******************************************************************************
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!
*******************************************************************************
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!
*******************************************************************************
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!
*******************************************************************************
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!
*******************************************************************************
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!
*******************************************************************************
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!
*******************************************************************************
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!
*******************************************************************************
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!
*******************************************************************************
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!
*******************************************************************************
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!

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