MEME-5.0.0 installation error

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fanyi...@gmail.com

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Jun 11, 2018, 10:57:24 PM6/11/18

to MEME Suite Q&A

Hi guys,

I've tried to install MEME-5.0.0 on mac, with all the necessary dependencies, and have paid attention to Python version.

Now some of the functions like FIMO, AME are working, but I can't use 'fasta-get-markov'. It's shown as code not found. That's the command that I really wish could work.

Here are some basic information:

the MEME Suite version: 5.0.0
the OS version: 10.13.2
the autoconf version: autoconf (GNU Autoconf) 2.69
the compiler version: Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1; Apple LLVM version 9.1.0 (clang-902.0.39.2)
the Perl version:v5.26.2
the Python version: python2.7.13; python3.5.2 (I set the default to python2.7 during installation)

Errors were reported during 'make test' as shown below. In addition, test_suit.log, make.log, install.log, configure.log are also included.

Thank you very much!

Best wishes,

Fanying

###################### Here is the test.log ######################

cd tests/scripts; /Applications/Xcode.app/Contents/Developer/usr/bin/make check

/Applications/Xcode.app/Contents/Developer/usr/bin/make test_driver

/usr/bin/sed -e 's%@WHICHPERL@%/opt/local/bin/perl%' \

-e 's%@MYDISTDIR@%../..%' \

-e 's%@BUILDDIR@%../..%' \

-e 's%@TESTDIR@%../..%' test_driver.pl.in > test_driver

chmod +x test_driver

/Applications/Xcode.app/Contents/Developer/usr/bin/make check-TESTS

SKIP: motif-in.meme.crp0.text (meme.txt missing)

SKIP: motif-in.meme.crp0.xml (meme.xml missing)

SKIP: motif-in.meme.crp0.html (meme.html missing)

SKIP: motif-in.meme.lipocalin.text (meme.txt missing)

SKIP: motif-in.meme.lipocalin.xml (meme.xml missing)

SKIP: motif-in.meme.lipocalin.html (meme.html missing)

SKIP: motif-in.meme.puf3p.text (meme.txt missing)

SKIP: motif-in.meme.puf3p.xml (meme.xml missing)

SKIP: motif-in.meme.puf3p.html (meme.html missing)

SKIP: motif-in.meme.crp0.extdna.text (meme.txt missing)

SKIP: motif-in.meme.crp0.extdna.xml (meme.xml missing)

SKIP: motif-in.meme.crp0.extdna.html (meme.html missing)

PASS: motif-in.dreme.klf1.text

PASS: motif-in.dreme.klf1.xml

PASS: motif-in.dreme.klf1.html

PASS: motif-in.dreme.klf1.extdna.text

PASS: motif-in.dreme.klf1.extdna.xml

PASS: motif-in.dreme.klf1.extdna.html

PASS: motif-in.dreme.puf3p.text

PASS: motif-in.dreme.puf3p.xml

PASS: motif-in.dreme.puf3p.html

PASS: ama1

PASS: ama2

PASS: ame1

PASS: ame2

PASS: ame3

PASS: ame4

PASS: ame5

PASS: ame6

PASS: ame7

PASS: ame8

PASS: ame9

PASS: ame10

PASS: ame11

PASS: ame12

PASS: ame13

PASS: centrimo1

PASS: centrimo2

PASS: centrimo3

PASS: centrimo4

PASS: centrimo5

PASS: centrimo6

PASS: centrimo7

PASS: centrimo8

PASS: centrimo9

PASS: create-priors1

PASS: create-priors2

PASS: dreme1

PASS: dreme2

PASS: dreme3

PASS: dreme4

PASS: fasta-center1

PASS: fasta-dinucleotide-shuffle1

PASS: fimo1

PASS: fimo2

PASS: fimo3

PASS: fimo4

PASS: glam2_1

PASS: glam2scan1

PASS: gomo1

PASS: gomo2

PASS: mast1

PASS: mast2

PASS: mast3

PASS: mast4

PASS: mast5

PASS: mast6

PASS: mast7

PASS: mast8

PASS: mast9

PASS: mast10

PASS: mast11

PASS: mast12

PASS: mast13

PASS: mast14

PASS: mast15

PASS: mast16

PASS: mast17

PASS: mast18

PASS: mast19

PASS: mast20

PASS: mast21

PASS: mcast1

PASS: mcast2

FAIL: meme1 (CRASH!)

FAIL: meme2 (CRASH!)

FAIL: meme3 (CRASH!)

FAIL: meme4 (CRASH!)

FAIL: meme5 (CRASH!)

FAIL: meme6 (CRASH!)

FAIL: meme7 (CRASH!)

FAIL: meme8 (CRASH!)

FAIL: meme9 (CRASH!)

FAIL: meme10 (CRASH!)

FAIL: meme11 (CRASH!)

FAIL: meme12 (CRASH!)

FAIL: meme13 (CRASH!)

FAIL: meme14 (CRASH!)

FAIL: meme15 (CRASH!)

FAIL: meme16 (CRASH!)

FAIL: meme17 (CRASH!)

FAIL: meme18 (CRASH!)

FAIL: meme_psp (CRASH!)

PASS: meme-chip1

PASS: momo1

PASS: momo2

PASS: momo3

PASS: momo4

PASS: momo5

PASS: momo6

PASS: momo7

PASS: momo8

PASS: momo9

PASS: momo10

PASS: momo11

PASS: momo12

PASS: momo13

PASS: momo14

PASS: momo15

PASS: momo16

PASS: momo17

PASS: motiph1

PASS: motiph2

PASS: psp-gen1

PASS: psp-gen2

PASS: psp-gen3

PASS: qvalue1

PASS: qvalue2

PASS: spamo1

PASS: spamo2

PASS: spamo3

PASS: spamo4

PASS: tomtom1

PASS: tomtom_allr

PASS: tomtom_ed

PASS: tomtom_kullback

PASS: tomtom_pearson

PASS: tomtom_sandelin

PASS: tomtom_blic1

PASS: tomtom_blic5

PASS: tomtom_allr_cs

PASS: tomtom_ed_cs

PASS: tomtom_kullback_cs

PASS: tomtom_pearson_cs

PASS: tomtom_sandelin_cs

PASS: tomtom_blic1_cs

PASS: tomtom_blic5_cs

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

Testsuite summary for meme 5.0.0

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

# TOTAL: 147

# PASS: 116

# SKIP: 12

# XFAIL: 0

# FAIL: 19

# XPASS: 0

# ERROR: 0

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

See tests/scripts/test-suite.log

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

make[3]: *** [test-suite.log] Error 1

make[2]: *** [check-TESTS] Error 2

make[1]: *** [check-am] Error 2

make: *** [test] Error 2

###################### Here is test-suite.log:######################

reference centrimo/neg_pv_site_counts.txt output results/centrimo9/site_counts.txt

reference centrimo/neg_pv_centrimo.tsv output results/centrimo9/centrimo.tsv

reference centrimo/neg_pv_centrimo.html output results/centrimo9/centrimo.html

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

reference create-priors/priors.wig output results/create-priors1/priors.wig

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

reference create-priors/priors.dist output results/create-priors2/priors.dist

PASSED!

RUN: dreme

==========

*******************************************************************************

Test dreme1 ...

dreme -oc results/dreme1 -verbosity 1 -p common/Klf1-200-100.fa -n common/Klf1-200-100-shuffled.fa &> log

reference dreme/basic.xml output results/dreme1/dreme.xml

PASSED!

*******************************************************************************

Test dreme2 ...

dreme -norc -oc results/dreme2 -verbosity 1 -p common/Klf1-200-100.fa -n common/Klf1-200-100-shuffled.fa &> log

reference dreme/norc.xml output results/dreme2/dreme.xml

PASSED!

*******************************************************************************

Test dreme3 ...

dreme-py3 -oc results/dreme3 -verbosity 1 -p common/Klf1-200-100.fa -n common/Klf1-200-100-shuffled.fa &> log

reference dreme/basic.xml output results/dreme3/dreme.xml

PASSED!

*******************************************************************************

Test dreme4 ...

dreme-py3 -norc -oc results/dreme4 -verbosity 1 -p common/Klf1-200-100.fa -n common/Klf1-200-100-shuffled.fa &> log

reference dreme/norc.xml output results/dreme4/dreme.xml

PASSED!

RUN: fasta-center

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

*******************************************************************************

Test fasta-center1 ...

fasta-center -len 100 -dna < common/Klf1-200.fa 1> results/fasta-center1/fasta-center_KqrKG_stdout 2> log

reference common/Klf1-200-100.no_fasta.fa output results/fasta-center1/fasta-center_KqrKG_stdout

PASSED!

RUN: fasta-dinucleotide-shuffle

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

*******************************************************************************

Test fasta-dinucleotide-shuffle1 ...

fasta-dinucleotide-shuffle -f common/Klf1-200-100.fa -t -dinuc 1> results/fasta-dinucleotide-shuffle1/fasta-dinucleotide-shuffle_vlszz_stdout 2> log

reference common/Klf1-200-100-shuffled.fa output results/fasta-dinucleotide-shuffle1/fasta-dinucleotide-shuffle_vlszz_stdout

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=0.799106

reference fimo/fimo.tsv output results/fimo1/fimo.tsv

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.

reference fimo/fimo-motif23.tsv output results/fimo2/fimo.tsv

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

reference fimo/fimo-priors.tsv output results/fimo3/fimo.tsv

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

reference fimo/fimo-priors-genomic.tsv output results/fimo4/fimo.tsv

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

reference glam2/glam2.txt output results/glam2_1/glam2.txt

PASSED!

RUN: glam2scan

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

*******************************************************************************

Test glam2scan1 ...

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

The output directory 'results/glam2scan1' already exists.

Its contents will be overwritten.

reference glam2scan/glam2scan.txt output results/glam2scan1/glam2scan.txt

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

reference gomo/gomo.smallthreshold.tsv output results/gomo1/gomo.tsv

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

reference gomo/gomo.multipleSpecies.tsv output results/gomo2/gomo.tsv

PASSED!

RUN: mast

=========

*******************************************************************************

Test mast1 ...

mast meme/meme.crp0.classic.oops.txt common/crp0.s -oc results/mast1 -nostatus &> log

reference mast/mast.crp0.classic.oops.txt.xml output results/mast1/mast.xml

PASSED!

*******************************************************************************

Test mast2 ...

mast meme/meme.crp0.classic.zoops.xml common/crp0.s -oc results/mast2 -nostatus &> log

reference mast/mast.crp0.classic.zoops.xml.xml output results/mast2/mast.xml

PASSED!

*******************************************************************************

Test mast3 ...

mast meme/meme.crp0.classic.anr.html common/crp0.s -oc results/mast3 -nostatus &> log

reference mast/mast.crp0.classic.anr.html.xml output results/mast3/mast.xml

PASSED!

*******************************************************************************

Test mast4 ...

mast meme/meme.INO_up800.classic.oops.txt common/INO_up800.s -oc results/mast4 -nostatus &> log

reference mast/mast.INO_up800.classic.oops.txt.xml output results/mast4/mast.xml

PASSED!

*******************************************************************************

Test mast5 ...

mast meme/meme.INO_up800.classic.zoops.xml common/INO_up800.s -oc results/mast5 -nostatus &> log

reference mast/mast.INO_up800.classic.zoops.xml.xml output results/mast5/mast.xml

PASSED!

*******************************************************************************

Test mast6 ...

mast meme/meme.INO_up800.classic.anr.html common/INO_up800.s -oc results/mast6 -nostatus &> log

reference mast/mast.INO_up800.classic.anr.html.xml output results/mast6/mast.xml

PASSED!

*******************************************************************************

Test mast7 ...

mast meme/meme.farntrans5.classic.oops.txt common/farntrans5.s -oc results/mast7 -nostatus &> log

reference mast/mast.farntrans5.classic.oops.txt.xml output results/mast7/mast.xml

PASSED!

*******************************************************************************

Test mast8 ...

mast meme/meme.farntrans5.classic.zoops.xml common/farntrans5.s -oc results/mast8 -nostatus &> log

reference mast/mast.farntrans5.classic.zoops.xml.xml output results/mast8/mast.xml

PASSED!

*******************************************************************************

Test mast9 ...

mast meme/meme.farntrans5.classic.anr.html common/farntrans5.s -oc results/mast9 -nostatus &> log

reference mast/mast.farntrans5.classic.anr.html.xml output results/mast9/mast.xml

PASSED!

*******************************************************************************

Test mast10 ...

mast meme/meme.lipocalin.classic.oops.txt common/lipocalin.s -oc results/mast10 -nostatus &> log

reference mast/mast.lipocalin.classic.oops.txt.xml output results/mast10/mast.xml

PASSED!

*******************************************************************************

Test mast11 ...

mast meme/meme.lipocalin.classic.zoops.xml common/lipocalin.s -oc results/mast11 -nostatus &> log

reference mast/mast.lipocalin.classic.zoops.xml.xml output results/mast11/mast.xml

PASSED!

*******************************************************************************

Test mast12 ...

mast meme/meme.lipocalin.classic.anr.html common/lipocalin.s -oc results/mast12 -nostatus &> log

reference mast/mast.lipocalin.classic.anr.html.xml output results/mast12/mast.xml

PASSED!

*******************************************************************************

Test mast13 ...

mast meme/meme.adh.classic.oops.txt common/adh.s -oc results/mast13 -nostatus &> log

reference mast/mast.adh.classic.oops.txt.xml output results/mast13/mast.xml

PASSED!

*******************************************************************************

Test mast14 ...

mast meme/meme.adh.classic.oops.txt - -oc results/mast14 -nostatus -df stdin -dna -seqp < common/mini-drosoph.s &> log

reference mast/mast.adh.classic.oops.mini-drosoph.txt.xml output results/mast14/mast.xml

PASSED!

*******************************************************************************

Test mast15 ...

mast meme/meme.adh.classic.zoops.html common/adh.s -oc results/mast15 -nostatus &> log

reference mast/mast.adh.classic.zoops.html.xml output results/mast15/mast.xml

PASSED!

*******************************************************************************

Test mast16 ...

mast meme/meme.adh.classic.zoops.html - -oc results/mast16 -nostatus -df stdin -dna -seqp < common/mini-drosoph.s &> log

reference mast/mast.adh.classic.zoops.mini-drosoph.html.xml output results/mast16/mast.xml

PASSED!

*******************************************************************************

Test mast17 ...

mast meme/meme.adh.classic.anr.xml common/adh.s -oc results/mast17 -nostatus &> log

reference mast/mast.adh.classic.anr.xml.xml output results/mast17/mast.xml

PASSED!

*******************************************************************************

Test mast18 ...

mast meme/meme.adh.classic.anr.xml - -oc results/mast18 -nostatus -df stdin -dna -seqp < common/mini-drosoph.s &> log

reference mast/mast.adh.classic.anr.mini-drosoph.xml.xml output results/mast18/mast.xml

PASSED!

*******************************************************************************

Test mast19 ...

mast meme/meme.INO_up800.classic.anr.txt common/INO_up800.s -oc results/mast19 -nostatus &> log

reference mast/mast.INO_up800.classic.anr.html.html output results/mast19/mast.html

PASSED!

*******************************************************************************

Test mast20 ...

mast meme/meme.INO_up800.classic.anr.xml common/INO_up800.s -oc results/mast20 -nostatus &> log

reference mast/mast.INO_up800.classic.anr.html.html output results/mast20/mast.html

PASSED!

*******************************************************************************

Test mast21 ...

mast meme/meme.INO_up800.classic.anr.html common/INO_up800.s -oc results/mast21 -nostatus &> log

reference mast/mast.INO_up800.classic.anr.html.html output results/mast21/mast.html

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 | 22-23-24-25-26-27-28-29-30-31-32-33-34-35-36-37-38-39-40-41 | (42)

Reading sequences in blocks of 232558 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: 0.002676 seconds

System time for computation: 0.000417 seconds

User time for output: 0.001825 seconds

System time for output: 0.002857 seconds

Total user time: 0.004501 seconds

Total system time: 0.003274 seconds

reference mcast/lex0.zoops.tsv output results/mcast1/mcast.tsv

reference mcast/lex0.zoops.gff output results/mcast1/mcast.gff

reference mcast/lex0.zoops.xml output results/mcast1/mcast.xml

reference mcast/lex0.zoops.cisml output results/mcast1/cisml.xml

reference mcast/lex0.zoops.html output results/mcast1/mcast.html

PASSED!

*******************************************************************************

Test mcast2 ...

mcast -oc results/mcast2 -parse-genomic-coord fimo/GCN4.meme.txt fimo/GCN4_YPD-genomic.fasta &> 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 | 23-24-25-26-27-28-29-30-31-32-33-34-35-36-37-38-39-40-41-42-43 | (44)

Reading sequences in blocks of 222222 characters.

Warning: Cannot estimate pi_0 accurately from fewer than 100 p-values. total p-values = 34. Using pi_zero = 1.0.

User time for computation: 0.009959 seconds

System time for computation: 0.001052 seconds

User time for output: 0.001817 seconds

System time for output: 0.002925 seconds

Total user time: 0.011776 seconds

Total system time: 0.003977 seconds

reference mcast/parse_genomic.tsv output results/mcast2/mcast.tsv

reference mcast/parse_genomic.gff output results/mcast2/mcast.gff

reference mcast/parse_genomic.xml output results/mcast2/mcast.xml

reference mcast/parse_genomic.cisml output results/mcast2/cisml.xml

reference mcast/parse_genomic.html output results/mcast2/mcast.html

PASSED!

RUN: meme

=========

*******************************************************************************

Test meme1 ...

meme -p 5 common/crp0.s -oc results/meme1 -mod oops -dna -revcomp -nmotifs 2 -objfun classic -minw 8 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme2 ...

meme -p 5 common/crp0.s -oc results/meme2 -mod zoops -dna -revcomp -nmotifs 2 -objfun classic -minw 8 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme3 ...

meme -p 5 common/crp0.s -oc results/meme3 -mod anr -dna -revcomp -nmotifs 2 -objfun classic -minw 8 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme4 ...

meme -p 5 common/adh.s -oc results/meme4 -mod oops -protein -nmotifs 2 -objfun classic -minw 8 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme5 ...

meme -p 5 common/adh.s -oc results/meme5 -mod zoops -protein -nmotifs 2 -objfun classic -minw 8 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme6 ...

meme -p 5 common/adh.s -oc results/meme6 -mod anr -protein -nmotifs 2 -objfun classic -minw 8 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme7 ...

meme -p 5 -csites 30 common/Klf1-200-100.fa -oc results/meme7 -mod oops -dna -revcomp -brief 0 -nmotifs 2 -objfun classic -minw 8 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme8 ...

meme -p 5 -csites 30 common/Klf1-200-100.fa -oc results/meme8 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun classic -minw 8 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme9 ...

meme -p 5 -csites 30 common/Klf1-200-100.fa -oc results/meme9 -mod anr -dna -revcomp -brief 0 -nmotifs 2 -objfun classic -minw 8 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme10 ...

meme -p 5 common/crp0.s -oc results/meme10 -mod oops -dna -revcomp -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme11 ...

meme -p 5 common/crp0.s -oc results/meme11 -mod zoops -dna -revcomp -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme12 ...

meme -p 5 common/crp0.s -oc results/meme12 -mod anr -dna -revcomp -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme13 ...

meme -p 5 common/adh.s -oc results/meme13 -mod oops -protein -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme14 ...

meme -p 5 common/adh.s -oc results/meme14 -mod zoops -protein -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme15 ...

meme -p 5 common/adh.s -oc results/meme15 -mod anr -protein -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme16 ...

meme -p 5 common/Klf1-200-100.fa -oc results/meme16 -mod oops -dna -revcomp -brief 0 -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme17 ...

meme -p 5 common/Klf1-200-100.fa -oc results/meme17 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme18 ...

meme -p 5 common/Klf1-200-100.fa -oc results/meme18 -mod anr -dna -revcomp -brief 0 -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 indicating failure.

FAILED!

*******************************************************************************

Test meme_psp ...

meme -p 5 common/psp_test.s -oc results/meme19 -psp common/psp_test.psp -minsites 5 -dna -revcomp -minw 7 -maxw 12 -nostatus -searchsize 0 &> log

--------------------------------------------------------------------------

There are not enough slots available in the system to satisfy the 5 slots

that were requested by the application:

/Users/fanyingtang/Documents/meme-5.0.0/src/parallel/meme

Either request fewer slots for your application, or make more slots available

for use.

--------------------------------------------------------------------------

-------------------------------------------------------------------------------

meme exited with value 1 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.fa &> log

Starting getsize: getsize results/meme-chip1/Klf1.100.fa 1> $metrics

getsize ran successfully in 0.011785 seconds

Starting fasta-most: fasta-most -min 50 < results/meme-chip1/Klf1.100.fa 1> $metrics

fasta-most ran successfully in 0.052109 seconds

Starting fasta-center: fasta-center -dna -len 100 < results/meme-chip1/Klf1.100.fa 1> results/meme-chip1/seqs-centered

fasta-center ran successfully in 0.058652 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 0.00956 seconds

Starting fasta-get-markov: fasta-get-markov -nostatus -nosummary -dna -m 1 results/meme-chip1/Klf1.100.fa results/meme-chip1/background

fasta-get-markov ran successfully in 0.00905 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 ran successfully in 20.149956 seconds

Starting dreme: dreme -verbosity 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 1.803396 seconds

Starting centrimo: centrimo -seqlen 500 -verbosity 1 -oc results/meme-chip1/centrimo_out -bfile results/meme-chip1/background results/meme-chip1/Klf1.100.fa results/meme-chip1/meme_out/meme.xml results/meme-chip1/dreme_out/dreme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme

centrimo ran successfully in 0.558348 seconds

Starting tomtom: tomtom -verbosity 1 -oc results/meme-chip1/meme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc results/meme-chip1/meme_out/meme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme

tomtom ran successfully in 2.039653 seconds

Starting tomtom: tomtom -verbosity 1 -oc results/meme-chip1/dreme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc results/meme-chip1/dreme_out/dreme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme

tomtom ran successfully in 0.22868 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 0.10786 seconds

Starting spamo: spamo -verbosity 1 -oc results/meme-chip1/spamo_out_1 -bgfile results/meme-chip1/background -keepprimary -primary WGGGYGTGGY results/meme-chip1/Klf1.100.fa results/meme-chip1/meme_out/meme.xml results/meme-chip1/meme_out/meme.xml results/meme-chip1/dreme_out/dreme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme

spamo ran successfully in 1.390584 seconds

Starting spamo: spamo -verbosity 1 -oc results/meme-chip1/spamo_out_2 -bgfile results/meme-chip1/background -keepprimary -primary WGCYYCHBCCCTCYC results/meme-chip1/Klf1.100.fa results/meme-chip1/meme_out/meme.xml results/meme-chip1/meme_out/meme.xml results/meme-chip1/dreme_out/dreme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme

spamo ran successfully in 0.701274 seconds

Starting spamo: spamo -verbosity 1 -oc results/meme-chip1/spamo_out_3 -bgfile results/meme-chip1/background -keepprimary -primary MA0140.2 results/meme-chip1/Klf1.100.fa meme-chip/JASPAR_CORE_2014_vertebrates.meme results/meme-chip1/meme_out/meme.xml results/meme-chip1/dreme_out/dreme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme

spamo ran successfully in 0.58868 seconds

Starting fimo: fimo --parse-genomic-coord --verbosity 1 --oc results/meme-chip1/fimo_out_1 --bgfile results/meme-chip1/background --motif WGGGYGTGGY results/meme-chip1/meme_out/meme.xml results/meme-chip1/Klf1.100.fa

fimo ran successfully in 0.075952 seconds

Starting fimo: fimo --parse-genomic-coord --verbosity 1 --oc results/meme-chip1/fimo_out_2 --bgfile results/meme-chip1/background --motif WGCYYCHBCCCTCYC results/meme-chip1/meme_out/meme.xml results/meme-chip1/Klf1.100.fa

fimo ran successfully in 0.077051 seconds

Starting fimo: fimo --parse-genomic-coord --verbosity 1 --oc results/meme-chip1/fimo_out_3 --bgfile results/meme-chip1/background --motif MA0140.2 meme-chip/JASPAR_CORE_2014_vertebrates.meme results/meme-chip1/Klf1.100.fa

fimo ran successfully in 0.120646 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 -oc results/meme-chip1 -db meme-chip/JASPAR_CORE_2014_vertebrates.meme meme-chip/Klf1.100.fa" 5.0.0 "Thu Jun 07 12\:52\:48 2018 -0700"

meme-chip_html_to_tsv ran successfully in 0.150864 seconds

reference meme-chip/meme-chip.html output results/meme-chip1/meme-chip.html

reference meme-chip/summary.tsv output results/meme-chip1/summary.tsv

reference meme-chip/combined.meme output results/meme-chip1/combined.meme

PASSED!

RUN: momo

=========

*******************************************************************************

Test momo1 ...

momo simple --oc results/momo1 --sequence-column sequence momo/small-tide-mod.txt &> log

reference momo/default-no-fasta.txt output results/momo1/momo.txt

reference momo/default-no-fasta.html output results/momo1/momo.html

PASSED!

*******************************************************************************

Test momo2 ...

momo simple --oc results/momo2 --psm-type tide --protein-database momo/small-yeast.fasta --width 11 momo/small-tide-mod.txt &> log

reference momo/default-with-fasta.txt output results/momo2/momo.txt

reference momo/default-with-fasta.html output results/momo2/momo.html

PASSED!

*******************************************************************************

Test momo3 ...

momo simple --oc results/momo3 --psm-type tide --single-motif-per-mass T momo/small-tide-mod.txt &> log

reference momo/single-motif-per-mass.txt output results/momo3/momo.txt

reference momo/single-motif-per-mass.html output results/momo3/momo.html

PASSED!

*******************************************************************************

Test momo4 ...

momo simple --oc results/momo4 --psm-type tide --protein-database momo/small-yeast.fasta --width 11 --hash-fasta 0 momo/small-tide-mod.txt &> log

reference momo/default-with-fasta.txt output results/momo4/momo.txt

reference momo/default-with-fasta.html output results/momo4/momo.html

PASSED!

*******************************************************************************

Test momo5 ...

momo simple --oc results/momo5 --psm-type tide --eliminate-repeats 3 --protein-database momo/small-yeast.fasta momo/small-tide-mod.txt &> log

reference momo/elim3.txt output results/momo5/momo.txt

reference momo/elim3.html output results/momo5/momo.html

PASSED!

*******************************************************************************

Test momo6 ...

momo simple --oc results/momo6 --psm-type tide --eliminate-repeats 0 momo/small-tide-mod.txt &> log

reference momo/elim0.txt output results/momo6/momo.txt

reference momo/elim0.html output results/momo6/momo.html

PASSED!

*******************************************************************************

Test momo7 ...

momo simple --oc results/momo7 --psm-type tide --filter "xcorr rank,le,3" momo/small-tide-mod.txt &> log

reference momo/filterxcorrrankle3.txt output results/momo7/momo.txt

reference momo/filterxcorrrankle3.html output results/momo7/momo.html

PASSED!

*******************************************************************************

Test momo8 ...

momo simple --oc results/momo8 --protein-database momo/small-yeast.fasta momo/small-tide-mod-phospho.txt &> log

reference momo/default-with-fasta-no-mass-in-motif-names.txt output results/momo8/momo.txt

reference momo/default-with-fasta-no-mass-in-motif-names.html output results/momo8/momo.html

PASSED!

*******************************************************************************

Test momo9 ...

momo simple --oc results/momo9 --protein-database momo/small-yeast.fasta momo/small-tide-mod-phospho.fasta &> log

reference momo/default-with-fasta-no-mass-in-motif-names.txt output results/momo9/momo.txt

reference momo/default-with-fasta-no-mass-in-motif-names.html output results/momo9/momo.html

PASSED!

*******************************************************************************

Test momo10 ...

momo simple --oc results/momo10 --psm-type tide momo/small-tide-mod-1-out-of-2.txt momo/small-tide-mod-2-out-of-2.txt &> log

reference momo/default-no-fasta.txt output results/momo10/momo.txt

reference momo/default-no-fasta.html output results/momo10/momo.html

PASSED!

*******************************************************************************

Test momo11 ...

momo motifx --oc results/momo11 --psm-type tide --protein-database momo/small-yeast.fasta --score-threshold 0.05 --count-threshold 1 momo/small-tide-mod.txt &> log

reference momo/mtfx-s0.05-c1.txt output results/momo11/momo.txt

reference momo/mtfx-s0.05-c1.html output results/momo11/momo.html

PASSED!

*******************************************************************************

Test momo12 ...

momo motifx --oc results/momo12 --psm-type tide --protein-database momo/small-yeast.fasta --score-threshold 0.05 --count-threshold 1 --single-motif-per-mass T momo/small-tide-mod.txt &> log

reference momo/mtfx-s0.05-c1-smpmT.txt output results/momo12/momo.txt

reference momo/mtfx-s0.05-c1-smpmT.html output results/momo12/momo.html

PASSED!

*******************************************************************************

Test momo13 ...

momo motifx --oc results/momo13 --protein-database momo/small-yeast.fasta --score-threshold 0.05 --count-threshold 1 momo/small-tide-mod-phospho.txt &> log

reference momo/mtfx-s0.05-c1-no-mass-in-motif-names.txt output results/momo13/momo.txt

reference momo/mtfx-s0.05-c1-no-mass-in-motif-names.html output results/momo13/momo.html

PASSED!

*******************************************************************************

Test momo14 ...

momo motifx --oc results/momo14 --protein-database momo/small-yeast-prealigned-no-unknowns.txt --score-threshold 0.05 --count-threshold 1 momo/small-tide-mod-phospho.txt &> log

reference momo/mtfx-s0.05-c1-no-mass-in-motif-names-bg-kmers-only-bgfreqs.txt output results/momo14/momo.txt

reference momo/mtfx-s0.05-c1-no-mass-in-motif-names-bg-kmers-only-bgfreqs.html output results/momo14/momo.html

PASSED!

*******************************************************************************

Test momo15 ...

momo simple --oc results/momo15 --psm-type ms-gf+ --sequence-column Peptide momo/small-msgf-mod.txt &> log

reference momo/default-msgf-no-fasta.txt output results/momo15/momo.txt

reference momo/default-msgf-no-fasta.html output results/momo15/momo.html

PASSED!

*******************************************************************************

Test momo16 ...

momo simple --oc results/momo16 --psm-type comet --sequence-column "modified sequence" momo/small-comet-mod.txt &> log

reference momo/default-comet-no-fasta.txt output results/momo16/momo.txt

reference momo/default-comet-no-fasta.html output results/momo16/momo.html

PASSED!

*******************************************************************************

Test momo17 ...

momo modl --oc results/momo17 --psm-type tide --protein-database momo/small-yeast.fasta momo/small-tide-mod.txt &> log

reference momo/modl-default.txt output results/momo17/momo.txt

reference momo/modl-default.html output results/momo17/momo.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=0.812612

Total number of positions scored: 1758

reference motiph/motiph.gff output results/motiph1/motiph.txt

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

reference motiph/motiph-motif23.gff output results/motiph2/motiph.txt

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_LqO4w_stdout 2> log

reference psp-gen/one-peak-dna-revcomp.psp output results/pspgen1/psp-gen_LqO4w_stdout

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_8Apxh_stdout 2> log

reference psp-gen/one-peak-protein.psp output results/pspgen2/psp-gen_8Apxh_stdout

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_uezvK_stdout 2> log

reference psp-gen/one-peak-dna-revcomp.psp output results/pspgen1/psp-gen_uezvK_stdout

PASSED!

RUN: qvalue

===========

*******************************************************************************

Test qvalue1 ...

qvalue --header 1 --append --column 2 --seed 7718 qvalue/uniform.txt 1> results/qvalue1/qvalue_hq397_stdout 2> log

Read 1000 values from qvalue/uniform.txt.

reference qvalue/uniform.out output results/qvalue1/qvalue_hq397_stdout

PASSED!

*******************************************************************************

Test qvalue2 ...

qvalue --null qvalue/null.txt qvalue/observed.txt 1> results/qvalue2/qvalue_xeyPM_stdout 2> log

Read 5 values from qvalue/observed.txt.

Read 10 values from qvalue/null.txt.

Converting scores to p-values.

reference qvalue/observed.out output results/qvalue2/qvalue_xeyPM_stdout

PASSED!

RUN: spamo

==========

*******************************************************************************

Test spamo1 ...

spamo -oc results/spamo1 -verbosity 1 -margin 20 -shared 1 -bgfile --uniform-- spamo/limits.fasta spamo/primary.meme spamo/secondary.meme &> log

reference spamo/limits.html output results/spamo1/spamo.html

reference spamo/limits.tsv output results/spamo1/spamo.tsv

PASSED!

*******************************************************************************

Test spamo2 ...

spamo -oc results/spamo2 -verbosity 1 -margin 20 -shared 1 -bgfile --motif-- spamo/random.fasta spamo/primary.meme spamo/secondary.meme &> log

reference spamo/random.html output results/spamo2/spamo.html

reference spamo/random.tsv output results/spamo2/spamo.tsv

PASSED!

*******************************************************************************

Test spamo3 ...

spamo -oc results/spamo3 -verbosity 3 -xalph -primary TGCm1C -keepprimary -margin 20 -shared 1 -inc MA00\* -inc T\* -exc MA007\* common/dna_with_covalent.fa common/dna_with_covalent.meme common/Jaspar-subset.meme common/dna_with_covalent.meme common/dna_with_covalent.meme &> log

The output directory 'results/spamo3' already exists.

Its contents will be overwritten.

Loading Primary Motif (name=TGCm1C)

Loading All Sequences

Loaded 2499 Sequences

Determining Best Primary Matches

Eliminating Sequences Without Primary Matches

Eliminated 1553 Sequences Without Primary Match

Trimming Sequences

Freeing Unneeded Sequences

Loading Secondary Motifs from file 'common/Jaspar-subset.meme'

Discarding motif 'MA0140.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.

Discarding motif 'MA0079.1' in 'common/Jaspar-subset.meme' it matched an -exc pattern.

Discarding motif 'MA0079.2' in 'common/Jaspar-subset.meme' it matched an -exc pattern.

Discarding motif 'MA0163.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.

Discarding motif 'MA0270.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.

Discarding motif 'MA0300.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.

Discarding motif 'MA0309.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.

Discarding motif 'MA0443.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.

Loading Secondary Motifs from file 'common/dna_with_covalent.meme'

Discarding motif 'CCTTCC' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.

Discarding motif 'GCAGCA' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.

Discarding motif 'GCAm1C' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.

Discarding motif 'GCAm7C' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.

Discarding motif 'GCm1C1' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.

Discarding motif 'Gm1TGC' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.

Discarding motif 'Gm7GCA' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.

Discarding motif 'TGCmGC' in file 'common/dna_with_covalent.meme' (non-unique ID).

Warning: The following secondary motifs in 'common/dna_with_covalent.meme' were excluded as they didn't fit in the margin:

Tm1m1m1m1m1m1m1m1m1m1m1m1