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Vanessa
Nov 28, 2017, 1:09:33 PM11/28/17
to MEME Suite Q&A
Hi,
I am trying to install meme-suite to my Ubuntu 16.04 LTS lap top. I've tried this several different times and iterations and I can't seem to get it to work.
I have python version 2.7.12. I also went through and did the perl dependencies.pl. I then ran sudo cpan Math::CDF and sudo apt-get install libexpat1-dev. I also did sudo apt-get install zlib1g-dev as well as sudo apt-get install autoconf sudo apt-get install automake sudo apt-get install libtool.
I ran: ./configure --prefix=$HOME/meme --with-url=http://meme-suite.org --enable-build-libxml2 --enable-build-libxslt --with-python=/home/vanessa/bin/python
then make clean (since I've tried this now multiple times)
then make
and then make test
However, I still get the following errors (see below). Also, even after doing the sudo cpan Math::CDF and sudo apt-get install libexpat1-dev when I run perl dependencies.pl it's still saying I have missing components. I also don't have a 'meme' folder anywhere in my HOME folder.
perl dependencies.pl
Checking Required Perl Modules:
HTML::Template missing.
JSON missing.
XML::Simple missing.
XML::Compile::SOAP11 missing. Used for downloading sequence databases from RSAT
XML::Compile::WSDL11 missing. Used for downloading sequence databases from RSAT
XML::Compile::Transport::SOAPHTTP missing. Used for downloading sequence databases from RSAT
Checking Optional Modules:
Log::Log4perl missing. Used for logging and debugging by developers.
From make test:
vanessa@DIV:~/meme_4.12.0$ make test
cp -f src/parallel/meme src/meme; \
cp -f src/parallel/momo src/momo; \
cd tests/scripts; make check
make[1]: Entering directory '/home/vanessa/meme_4.12.0/tests/scripts'
make test_driver
make[2]: Entering directory '/home/vanessa/meme_4.12.0/tests/scripts'
/bin/sed -e 's%@WHICHPERL@%/usr/bin/perl%' test_driver.pl.in > test_driver
chmod +x test_driver
make[2]: Leaving directory '/home/vanessa/meme_4.12.0/tests/scripts'
make check-TESTS
make[2]: Entering directory '/home/vanessa/meme_4.12.0/tests/scripts'
make[3]: Entering directory '/home/vanessa/meme_4.12.0/tests/scripts'
PASS: ama1
PASS: ama2
PASS: ame1
PASS: centrimo1
PASS: create-priors1
PASS: create-priors2
ERROR: /home/vanessa/meme_4.12.0/tests/scripts/dreme.test (FAULT IN TEST!)
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: mcast1
PASS: meme1
PASS: meme2
PASS: meme3
PASS: meme4
PASS: meme5
PASS: meme6
PASS: meme_psp
FAIL: meme-chip1 (CRASH!)
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: motif-in.meme.crp0.text
PASS: motif-in.meme.crp0.xml
PASS: motif-in.meme.crp0.html
PASS: motif-in.meme.lipocalin.text
PASS: motif-in.meme.lipocalin.xml
PASS: motif-in.meme.lipocalin.html
PASS: motif-in.meme.puf3p.text
PASS: motif-in.meme.puf3p.xml
PASS: motif-in.meme.puf3p.html
PASS: motif-in.meme.crp0.extdna.text
PASS: motif-in.meme.crp0.extdna.xml
PASS: motif-in.meme.crp0.extdna.html
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: motiph1
PASS: motiph2
PASS: psp-gen1
PASS: psp-gen2
PASS: psp-gen3
PASS: qvalue1
PASS: qvalue2
PASS: spamo1
PASS: spamo2
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 4.12.0
============================================================================
# TOTAL: 105
# PASS: 103
# SKIP: 0
# XFAIL: 0
# FAIL: 1
# XPASS: 0
# ERROR: 1
============================================================================
See tests/scripts/test-suite.log
============================================================================
Makefile:572: recipe for target 'test-suite.log' failed
make[3]: *** [test-suite.log] Error 1
make[3]: Leaving directory '/home/vanessa/meme_4.12.0/tests/scripts'
Makefile:678: recipe for target 'check-TESTS' failed
make[2]: *** [check-TESTS] Error 2
make[2]: Leaving directory '/home/vanessa/meme_4.12.0/tests/scripts'
Makefile:744: recipe for target 'check-am' failed
make[1]: *** [check-am] Error 2
make[1]: Leaving directory '/home/vanessa/meme_4.12.0/tests/scripts'
Makefile:1185: recipe for target 'test' failed
make: *** [test] Error 2
I am trying to install meme-suite to my Ubuntu 16.04 LTS lap top. I've tried this several different times and iterations and I can't seem to get it to work.
I have python version 2.7.12. I also went through and did the perl dependencies.pl. I then ran sudo cpan Math::CDF and sudo apt-get install libexpat1-dev. I also did sudo apt-get install zlib1g-dev as well as sudo apt-get install autoconf sudo apt-get install automake sudo apt-get install libtool.
I ran: ./configure --prefix=$HOME/meme --with-url=http://meme-suite.org --enable-build-libxml2 --enable-build-libxslt --with-python=/home/vanessa/bin/python
then make clean (since I've tried this now multiple times)
then make
and then make test
However, I still get the following errors (see below). Also, even after doing the sudo cpan Math::CDF and sudo apt-get install libexpat1-dev when I run perl dependencies.pl it's still saying I have missing components. I also don't have a 'meme' folder anywhere in my HOME folder.
perl dependencies.pl
Checking Required Perl Modules:
HTML::Template missing.
JSON missing.
XML::Simple missing.
XML::Compile::SOAP11 missing. Used for downloading sequence databases from RSAT
XML::Compile::WSDL11 missing. Used for downloading sequence databases from RSAT
XML::Compile::Transport::SOAPHTTP missing. Used for downloading sequence databases from RSAT
Checking Optional Modules:
Log::Log4perl missing. Used for logging and debugging by developers.
From make test:
vanessa@DIV:~/meme_4.12.0$ make test
cp -f src/parallel/meme src/meme; \
cp -f src/parallel/momo src/momo; \
cd tests/scripts; make check
make[1]: Entering directory '/home/vanessa/meme_4.12.0/tests/scripts'
make test_driver
make[2]: Entering directory '/home/vanessa/meme_4.12.0/tests/scripts'
/bin/sed -e 's%@WHICHPERL@%/usr/bin/perl%' test_driver.pl.in > test_driver
chmod +x test_driver
make[2]: Leaving directory '/home/vanessa/meme_4.12.0/tests/scripts'
make check-TESTS
make[2]: Entering directory '/home/vanessa/meme_4.12.0/tests/scripts'
make[3]: Entering directory '/home/vanessa/meme_4.12.0/tests/scripts'
PASS: ama1
PASS: ama2
PASS: ame1
PASS: centrimo1
PASS: create-priors1
PASS: create-priors2
ERROR: /home/vanessa/meme_4.12.0/tests/scripts/dreme.test (FAULT IN TEST!)
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: mcast1
PASS: meme1
PASS: meme2
PASS: meme3
PASS: meme4
PASS: meme5
PASS: meme6
PASS: meme_psp
FAIL: meme-chip1 (CRASH!)
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: motif-in.meme.crp0.text
PASS: motif-in.meme.crp0.xml
PASS: motif-in.meme.crp0.html
PASS: motif-in.meme.lipocalin.text
PASS: motif-in.meme.lipocalin.xml
PASS: motif-in.meme.lipocalin.html
PASS: motif-in.meme.puf3p.text
PASS: motif-in.meme.puf3p.xml
PASS: motif-in.meme.puf3p.html
PASS: motif-in.meme.crp0.extdna.text
PASS: motif-in.meme.crp0.extdna.xml
PASS: motif-in.meme.crp0.extdna.html
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: motiph1
PASS: motiph2
PASS: psp-gen1
PASS: psp-gen2
PASS: psp-gen3
PASS: qvalue1
PASS: qvalue2
PASS: spamo1
PASS: spamo2
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 4.12.0
============================================================================
# TOTAL: 105
# PASS: 103
# SKIP: 0
# XFAIL: 0
# FAIL: 1
# XPASS: 0
# ERROR: 1
============================================================================
See tests/scripts/test-suite.log
============================================================================
Makefile:572: recipe for target 'test-suite.log' failed
make[3]: *** [test-suite.log] Error 1
make[3]: Leaving directory '/home/vanessa/meme_4.12.0/tests/scripts'
Makefile:678: recipe for target 'check-TESTS' failed
make[2]: *** [check-TESTS] Error 2
make[2]: Leaving directory '/home/vanessa/meme_4.12.0/tests/scripts'
Makefile:744: recipe for target 'check-am' failed
make[1]: *** [check-am] Error 2
make[1]: Leaving directory '/home/vanessa/meme_4.12.0/tests/scripts'
Makefile:1185: recipe for target 'test' failed
make: *** [test] Error 2
cegrant
Nov 28, 2017, 5:36:49 PM11/28/17
to MEME Suite Q&A
perl dependencies.pl
Checking Required Perl Modules:
HTML::Template missing.
JSON missing.
XML::Simple missing.
XML::Compile::SOAP11 missing. Used for downloading sequence databases from RSAT
XML::Compile::WSDL11 missing. Used for downloading sequence databases from RSAT
XML::Compile::Transport::SOAPHTTP missing. Used for downloading sequence databases from RSAT
This is saying that your are still missing 3 required Perl modules. You have to install the modules
HTML::Template
JSON
XML::Simple
These modules are all available from CPAN.
The XML::Compile modules are optional and only used in setting up online sequence databases for a MEME Suite web site. You can safely ignore those.
In the tests/scripts directory you should find log files for each of the tests. The log files dreme.log and memechip.log should have more details about why the tests failed. I expect the errors are related to the missing Perl modules.
HTML::Template
JSON
XML::Simple
These modules are all available from CPAN.
The XML::Compile modules are optional and only used in setting up online sequence databases for a MEME Suite web site. You can safely ignore those.
In the tests/scripts directory you should find log files for each of the tests. The log files dreme.log and memechip.log should have more details about why the tests failed. I expect the errors are related to the missing Perl modules.
I also don't have a 'meme' folder anywhere in my HOME folder.
The meme folder won’t be created until you run ‘make install’.
Vanessa
Nov 29, 2017, 5:37:03 PM11/29/17
to MEME Suite Q&A
Hi there,
Thank you for the help. I'm still having some issues. This time when I run, perl dependencies.pl I don't get any errors (see below) - it's just blank this time.
Checking Required Perl Modules:
Checking Optional Modules:
However, when I run make test I'm having even more errors than in my previous post. I'm not sure how to interpret the log file errors or what to do next. If you have suggestions as to what to do next that would be so great. I really appreciate the help!
Thanks,
Vanessa
make test:
~/software/meme_4.12.0$ make test
Thank you for the help. I'm still having some issues. This time when I run, perl dependencies.pl I don't get any errors (see below) - it's just blank this time.
Checking Required Perl Modules:
Checking Optional Modules:
However, when I run make test I'm having even more errors than in my previous post. I'm not sure how to interpret the log file errors or what to do next. If you have suggestions as to what to do next that would be so great. I really appreciate the help!
Thanks,
Vanessa
make test:
~/software/meme_4.12.0$ make test
cp -f src/parallel/meme src/meme; \
cp -f src/parallel/momo src/momo; \
cd tests/scripts; make check
make[1]: Entering directory '/home/vanessa/software/meme_4.12.0/tests/scripts'
make test_driver
make[2]: Entering directory '/home/vanessa/software/meme_4.12.0/tests/scripts'
make test_driver
make[2]: Entering directory '/home/vanessa/software/meme_4.12.0/tests/scripts'
make[2]: Leaving directory '/home/vanessa/software/meme_4.12.0/tests/scripts'
make check-TESTS
make[2]: Entering directory '/home/vanessa/software/meme_4.12.0/tests/scripts'
make[3]: Entering directory '/home/vanessa/software/meme_4.12.0/tests/scripts'
make check-TESTS
make[2]: Entering directory '/home/vanessa/software/meme_4.12.0/tests/scripts'
make[3]: Entering directory '/home/vanessa/software/meme_4.12.0/tests/scripts'
PASS: ama1
PASS: ama2
PASS: ame1
PASS: centrimo1
PASS: create-priors1
PASS: create-priors2
ERROR: /home/vanessa/software/meme_4.12.0/tests/scripts/dreme.test (FAULT IN TEST!)
PASS: fasta-center1
FAIL: fasta-dinucleotide-shuffle1 (differences in stdout)
PASS: fasta-center1
FAIL: fasta-dinucleotide-shuffle1 (differences in stdout)
PASS: fimo1
PASS: fimo2
PASS: fimo3
PASS: fimo4
FAIL: glam2_1 (CRASH!)
FAIL: glam2scan1 (CRASH!)
FAIL: glam2scan1 (CRASH!)
FAIL: meme-chip1 (differences in combined.meme)
SKIP: motif-in.dreme.klf1.text (dreme.txt missing)
SKIP: motif-in.dreme.klf1.xml (dreme.xml missing)
SKIP: motif-in.dreme.klf1.html (dreme.html missing)
SKIP: motif-in.dreme.klf1.extdna.text (dreme.txt missing)
SKIP: motif-in.dreme.klf1.extdna.xml (dreme.xml missing)
SKIP: motif-in.dreme.klf1.extdna.html (dreme.html missing)
SKIP: motif-in.dreme.puf3p.text (dreme.txt missing)
SKIP: motif-in.dreme.puf3p.xml (dreme.xml missing)
SKIP: motif-in.dreme.puf3p.html (dreme.html missing)
SKIP: motif-in.dreme.klf1.xml (dreme.xml missing)
SKIP: motif-in.dreme.klf1.html (dreme.html missing)
SKIP: motif-in.dreme.klf1.extdna.text (dreme.txt missing)
SKIP: motif-in.dreme.klf1.extdna.xml (dreme.xml missing)
SKIP: motif-in.dreme.klf1.extdna.html (dreme.html missing)
SKIP: motif-in.dreme.puf3p.text (dreme.txt missing)
SKIP: motif-in.dreme.puf3p.xml (dreme.xml missing)
SKIP: motif-in.dreme.puf3p.html (dreme.html missing)
# TOTAL: 109
# PASS: 91
# SKIP: 9
# XFAIL: 0
# FAIL: 4
# XPASS: 0
# ERROR: 5
# PASS: 91
# SKIP: 9
# XFAIL: 0
# FAIL: 4
# XPASS: 0
# ERROR: 5
============================================================================
See tests/scripts/test-suite.log
============================================================================
Makefile:572: recipe for target 'test-suite.log' failed
make[3]: *** [test-suite.log] Error 1
make[3]: Leaving directory '/home/vanessa/software/meme_4.12.0/tests/scripts'
Makefile:678: recipe for target 'check-TESTS' failed
make[2]: *** [check-TESTS] Error 2
make[2]: Leaving directory '/home/vanessa/software/meme_4.12.0/tests/scripts'
Makefile:744: recipe for target 'check-am' failed
make[1]: *** [check-am] Error 2
make[1]: Leaving directory '/home/vanessa/software/meme_4.12.0/tests/scripts'
Makefile:1185: recipe for target 'test' failed
make: *** [test] Error 2
Here is what the dreme log error looks like,
Error parsing test /home/vanessavaraljay/software/meme_4.12.0/tests/scripts/dreme.test: Can't locate File/Which.pm in @INC (you may need to install the File::Which module) (@INC contains: /home/vanessavaraljay/software/meme_4.12.0/scripts /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /home/vanessavaraljay/software/meme_4.12.0/tests/scripts/dreme.test line 4.
BEGIN failed--compilation aborted at /home/vanessavaraljay/software/meme_4.12.0/tests/scripts/dreme.test line 4.
glam2 error log:
*******************************************************************************
Test glam2_1 ...
glam2 -M -r 3 -n 100 -O results/glam2_1 p common/At.s &> log
Writing results to output directory 'results/glam2_1'.
Run 1... 406 iterations
Run 2... 445 iterations
Run 3... 400 iterations
sh: 1: /home/vanessavaraljay/software/meme_4.12.0/scripts/glam2html: not found
Warning: failed to convert output to HTML!
sh: 1: /home/vanessavaraljay/software/meme_4.12.0/scripts/glam2psfm: not found
Warning: failed to convert output to MEME format motif!
-------------------------------------------------------------------------------
glam2 exited with value 1 indicating failure.
FAILED!
glam2 scan error log:
*******************************************************************************
Test glam2scan1 ...
glam2scan -O results/glam2scan1 p glam2/glam2.txt common/At.s &> log
Writing results to output directory 'results/glam2scan1'.
sh: 1: /home/vanessavaraljay/software/meme_4.12.0/scripts/glam2scan2html: not found
Warning: failed to convert output to HTML!
-------------------------------------------------------------------------------
glam2scan exited with value 1 indicating failure.
FAILED!
memechip error log:
*******************************************************************************
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 0.002076 seconds
Starting fasta-most: fasta-most -min 50 < results/meme-chip1/Klf1.100.s 1> $metrics
fasta-most ran successfully in 0.033808 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 0.041521 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 0.001903 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 0.001509 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 24.473226 seconds
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
Can't exec "/home/vanessavaraljay/software/meme_4.12.0/scripts/dreme": No such file or directory at /home/vanessavaraljay/software/meme_4.12.0/scripts/ExecUtils.pm line 156.
Exec failed at /home/vanessavaraljay/software/meme_4.12.0/scripts/ExecUtils.pm line 157.
at /home/vanessavaraljay/software/meme_4.12.0/scripts/meme-chip line 97.
main::__ANON__("Exec failed at /home/vanessavaraljay/software/meme_4.12.0/scr"...) called at /home/vanessavaraljay/software/meme_4.12.0/scripts/ExecUtils.pm line 157
ExecUtils::invoke("BIN", "/home/vanessavaraljay/software/meme_4.12.0/scripts", "ARGS", ARRAY(0x34c1330), "PROG", "dreme", "TIMEOUT", undef, "ALL_FILE", ...) called at /home/vanessavaraljay/software/meme_4.12.0/scripts/meme-chip line 556
main::run_job(HASH(0x3648688), HASH(0x36616f8), "dreme", ARRAY(0x3569b98), HASH(0x3569b50), 0, ARRAY(0x382c3d8)) called at /home/vanessavaraljay/software/meme_4.12.0/scripts/meme-chip line 986
main::dreme(HASH(0x3648688), HASH(0x36616f8), HASH(0x3776f30), HASH(0x37e77b0), HASH(0x3776b58), undef) called at /home/vanessavaraljay/software/meme_4.12.0/scripts/meme-chip line 1643
main::main() called at /home/vanessavaraljay/software/meme_4.12.0/scripts/meme-chip line 141
dreme exited with error code 2
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/meme_out/meme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme
centrimo ran successfully in 0.427151 seconds
Starting tomtom: tomtom -verbosity 1 -oc results/meme-chip1/meme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc -bfile results/meme-chip1/background results/meme-chip1/meme_out/meme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme
tomtom ran successfully in 1.038722 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 0.101858 seconds
Starting spamo: spamo -verbosity 1 -oc results/meme-chip1/spamo_out_1 -bgfile results/meme-chip1/background -primary WGGGYGTGGY results/meme-chip1/Klf1.100.s results/meme-chip1/meme_out/meme.xml results/meme-chip1/meme_out/meme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme
spamo ran successfully in 1.501944 seconds
Starting spamo: spamo -verbosity 1 -oc results/meme-chip1/spamo_out_2 -bgfile results/meme-chip1/background -primary WGCYYCHBCCCTCYC results/meme-chip1/Klf1.100.s results/meme-chip1/meme_out/meme.xml results/meme-chip1/meme_out/meme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme
spamo ran successfully in 1.491446 seconds
Starting spamo: spamo -verbosity 1 -oc results/meme-chip1/spamo_out_3 -bgfile results/meme-chip1/background -primary MA0140.2 results/meme-chip1/Klf1.100.s meme-chip/JASPAR_CORE_2014_vertebrates.meme results/meme-chip1/meme_out/meme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme
spamo ran successfully in 1.190347 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.s
fimo ran successfully in 0.04242 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.s
fimo ran successfully in 0.041674 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.s
fimo ran successfully in 0.083958 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 0.066044 seconds
-------------------------------------------------------------------------------
A difference was detected between the reference and tested json files.
Got data:programs@7:status=0 but expected data:programs@7:status=512.
4,11c4,10
< 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
---
> 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 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
> 6 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
> 7 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
> 8 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
> 9 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
38,49c38
< MOTIF 3 CACRCCC-DREME-1
<
< letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 3.0e-003
< 0.000000 1.000000 0.000000 0.000000
< 1.000000 0.000000 0.000000 0.000000
< 0.000000 1.000000 0.000000 0.000000
< 0.666667 0.000000 0.333333 0.000000
< 0.000000 1.000000 0.000000 0.000000
< 0.000000 1.000000 0.000000 0.000000
< 0.000000 1.000000 0.000000 0.000000
<
< MOTIF 4 MA0493.1-Klf1
---
> MOTIF 3 MA0493.1-Klf1
64c53
< MOTIF 5 MA0599.1-KLF5
---
> MOTIF 4 MA0599.1-KLF5
78c67
< MOTIF 6 WGCYYCHBCCCTCYC-MEME-2
---
> MOTIF 5 WGCYYCHBCCCTCYC-MEME-2
97c86
< MOTIF 7 MA0140.2-TAL1::GATA1
---
> MOTIF 6 MA0140.2-TAL1::GATA1
119c108
< MOTIF 8 MA0079.3-SP1
---
> MOTIF 7 MA0079.3-SP1
134c123
< MOTIF 9 MA0035.3-Gata1
---
> MOTIF 8 MA0035.3-Gata1
149c138
< MOTIF 10 MA0036.2-GATA2
---
> MOTIF 9 MA0036.2-GATA2
FAILED!
Error parsing test /home/vanessavaraljay/software/meme_4.12.0/tests/scripts/dreme.test: Can't locate File/Which.pm in @INC (you may need to install the File::Which module) (@INC contains: /home/vanessavaraljay/software/meme_4.12.0/scripts /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at /home/vanessavaraljay/software/meme_4.12.0/tests/scripts/dreme.test line 4.
BEGIN failed--compilation aborted at /home/vanessavaraljay/software/meme_4.12.0/tests/scripts/dreme.test line 4.
glam2 error log:
*******************************************************************************
Test glam2_1 ...
glam2 -M -r 3 -n 100 -O results/glam2_1 p common/At.s &> log
Writing results to output directory 'results/glam2_1'.
Run 1... 406 iterations
Run 2... 445 iterations
Run 3... 400 iterations
sh: 1: /home/vanessavaraljay/software/meme_4.12.0/scripts/glam2html: not found
Warning: failed to convert output to HTML!
sh: 1: /home/vanessavaraljay/software/meme_4.12.0/scripts/glam2psfm: not found
Warning: failed to convert output to MEME format motif!
-------------------------------------------------------------------------------
glam2 exited with value 1 indicating failure.
FAILED!
glam2 scan error log:
*******************************************************************************
Test glam2scan1 ...
glam2scan -O results/glam2scan1 p glam2/glam2.txt common/At.s &> log
Writing results to output directory 'results/glam2scan1'.
sh: 1: /home/vanessavaraljay/software/meme_4.12.0/scripts/glam2scan2html: not found
Warning: failed to convert output to HTML!
-------------------------------------------------------------------------------
glam2scan exited with value 1 indicating failure.
FAILED!
memechip error log:
*******************************************************************************
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 0.002076 seconds
Starting fasta-most: fasta-most -min 50 < results/meme-chip1/Klf1.100.s 1> $metrics
fasta-most ran successfully in 0.033808 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 0.041521 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 0.001903 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 0.001509 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 24.473226 seconds
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
Can't exec "/home/vanessavaraljay/software/meme_4.12.0/scripts/dreme": No such file or directory at /home/vanessavaraljay/software/meme_4.12.0/scripts/ExecUtils.pm line 156.
Exec failed at /home/vanessavaraljay/software/meme_4.12.0/scripts/ExecUtils.pm line 157.
at /home/vanessavaraljay/software/meme_4.12.0/scripts/meme-chip line 97.
main::__ANON__("Exec failed at /home/vanessavaraljay/software/meme_4.12.0/scr"...) called at /home/vanessavaraljay/software/meme_4.12.0/scripts/ExecUtils.pm line 157
ExecUtils::invoke("BIN", "/home/vanessavaraljay/software/meme_4.12.0/scripts", "ARGS", ARRAY(0x34c1330), "PROG", "dreme", "TIMEOUT", undef, "ALL_FILE", ...) called at /home/vanessavaraljay/software/meme_4.12.0/scripts/meme-chip line 556
main::run_job(HASH(0x3648688), HASH(0x36616f8), "dreme", ARRAY(0x3569b98), HASH(0x3569b50), 0, ARRAY(0x382c3d8)) called at /home/vanessavaraljay/software/meme_4.12.0/scripts/meme-chip line 986
main::dreme(HASH(0x3648688), HASH(0x36616f8), HASH(0x3776f30), HASH(0x37e77b0), HASH(0x3776b58), undef) called at /home/vanessavaraljay/software/meme_4.12.0/scripts/meme-chip line 1643
main::main() called at /home/vanessavaraljay/software/meme_4.12.0/scripts/meme-chip line 141
dreme exited with error code 2
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/meme_out/meme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme
centrimo ran successfully in 0.427151 seconds
Starting tomtom: tomtom -verbosity 1 -oc results/meme-chip1/meme_tomtom_out -min-overlap 5 -dist pearson -evalue -thresh 1 -no-ssc -bfile results/meme-chip1/background results/meme-chip1/meme_out/meme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme
tomtom ran successfully in 1.038722 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 0.101858 seconds
Starting spamo: spamo -verbosity 1 -oc results/meme-chip1/spamo_out_1 -bgfile results/meme-chip1/background -primary WGGGYGTGGY results/meme-chip1/Klf1.100.s results/meme-chip1/meme_out/meme.xml results/meme-chip1/meme_out/meme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme
spamo ran successfully in 1.501944 seconds
Starting spamo: spamo -verbosity 1 -oc results/meme-chip1/spamo_out_2 -bgfile results/meme-chip1/background -primary WGCYYCHBCCCTCYC results/meme-chip1/Klf1.100.s results/meme-chip1/meme_out/meme.xml results/meme-chip1/meme_out/meme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme
spamo ran successfully in 1.491446 seconds
Starting spamo: spamo -verbosity 1 -oc results/meme-chip1/spamo_out_3 -bgfile results/meme-chip1/background -primary MA0140.2 results/meme-chip1/Klf1.100.s meme-chip/JASPAR_CORE_2014_vertebrates.meme results/meme-chip1/meme_out/meme.xml meme-chip/JASPAR_CORE_2014_vertebrates.meme
spamo ran successfully in 1.190347 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.s
fimo ran successfully in 0.04242 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.s
fimo ran successfully in 0.041674 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.s
fimo ran successfully in 0.083958 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 0.066044 seconds
-------------------------------------------------------------------------------
A difference was detected between the reference and tested json files.
Got data:programs@7:status=0 but expected data:programs@7:status=512.
4,11c4,10
< 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
---
> 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 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
> 6 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
> 7 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
> 8 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
> 9 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
38,49c38
< MOTIF 3 CACRCCC-DREME-1
<
< letter-probability matrix: alength= 4 w= 7 nsites= 27 E= 3.0e-003
< 0.000000 1.000000 0.000000 0.000000
< 1.000000 0.000000 0.000000 0.000000
< 0.000000 1.000000 0.000000 0.000000
< 0.666667 0.000000 0.333333 0.000000
< 0.000000 1.000000 0.000000 0.000000
< 0.000000 1.000000 0.000000 0.000000
< 0.000000 1.000000 0.000000 0.000000
<
< MOTIF 4 MA0493.1-Klf1
---
> MOTIF 3 MA0493.1-Klf1
64c53
< MOTIF 5 MA0599.1-KLF5
---
> MOTIF 4 MA0599.1-KLF5
78c67
< MOTIF 6 WGCYYCHBCCCTCYC-MEME-2
---
> MOTIF 5 WGCYYCHBCCCTCYC-MEME-2
97c86
< MOTIF 7 MA0140.2-TAL1::GATA1
---
> MOTIF 6 MA0140.2-TAL1::GATA1
119c108
< MOTIF 8 MA0079.3-SP1
---
> MOTIF 7 MA0079.3-SP1
134c123
< MOTIF 9 MA0035.3-Gata1
---
> MOTIF 8 MA0035.3-Gata1
149c138
< MOTIF 10 MA0036.2-GATA2
---
> MOTIF 9 MA0036.2-GATA2
FAILED!
Vanessa
Nov 30, 2017, 10:03:09 AM11/30/17
to MEME Suite Q&A
Hi,
Never mind! I figured it out. I saw someone else's post on the forum in which they had the python path incorrect. I realized mine was too. Once I fixed that everything passed the make test.
Thanks,
Vanessa
Never mind! I figured it out. I saw someone else's post on the forum in which they had the python path incorrect. I realized mine was too. Once I fixed that everything passed the make test.
Thanks,
Vanessa
cegrant
Nov 30, 2017, 9:03:35 PM11/30/17
to MEME Suite Q&A
Glad you were able to figue it out! Let us know if you run into other problems.
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