Error installing MEME

[Daniel Hernández Bañuelos]

Hello, I have already installed the latest phyton and I dont get error in the make stage of installing MEME

In Make test i get this:

sudo 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/daniel/Descargas/meme_4.12.0/tests/scripts'
make  test_driver
make[2]: Entering directory '/home/daniel/Descargas/meme_4.12.0/tests/scripts'
make[2]: 'test_driver' is up to date.
make[2]: Leaving directory '/home/daniel/Descargas/meme_4.12.0/tests/scripts'
make  check-TESTS
make[2]: Entering directory '/home/daniel/Descargas/meme_4.12.0/tests/scripts'
make[3]: Entering directory '/home/daniel/Descargas/meme_4.12.0/tests/scripts'
PASS: ama1
PASS: ama2
PASS: ame1
PASS: centrimo1
PASS: create-priors1
PASS: create-priors2
ERROR: /home/daniel/Descargas/meme_4.12.0/tests/scripts/dreme.test (FAULT IN TEST!)
PASS: fasta-center1
FAIL: fasta-dinucleotide-shuffle1 (CRASH!)
PASS: fimo1
PASS: fimo2
PASS: fimo3
PASS: fimo4
FAIL: glam2_1 (CRASH!)
FAIL: glam2scan1 (CRASH!)
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 (differences in combined.meme)
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
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)
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:  91
# SKIP:  9
# XFAIL: 0
# FAIL:  4
# 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/daniel/Descargas/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/daniel/Descargas/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/daniel/Descargas/meme_4.12.0/tests/scripts'
Makefile:1185: recipe for target 'test' failed
make: *** [test] Error 2

HELP!!!

[CharlesEGrant]

Could your forward us a copy of config.log? This will let us see if there are any problems with the configuration. Also, if  you look in tests/scripts you should find a log file for each test with more information about why the test failed.  Take a look at fasta-dinucleotide-shuffle, glam2.log, glam2scan.log, and meme-chip.log to see more details about the problem. 

[Matthew Wright]

Hi,

I am getting the same test failures as Daniel (fasta-dinucleotide-shuffle1, glam2, glam2scan, and meme-chip). I think it is something related to Python.

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_z6mh9_stdout 2> log
Traceback (most recent call last):
  File "/home/matwright/Documents/meme-5.0.5/scripts/fasta-dinucleotide-shuffle", line 6, in <module>
    import alphabet
  File "/home/matwright/Documents/meme-5.0.5/scripts/alphabet.py", line 1096, in <module>
    predef = (dna(), rna(), protein())
  File "/home/matwright/Documents/meme-5.0.5/scripts/alphabet.py", line 1017, in dna
    factory.parseSymbol('A', "Adenine", 0xCC0000, complement='T')
  File "/home/matwright/Documents/meme-5.0.5/scripts/alphabet.py", line 451, in parseSymbol
    if not(isinstance(symbol, basestring) and len(symbol) == 1):
NameError: name 'basestring' is not defined
-------------------------------------------------------------------------------
fasta-dinucleotide-shuffle exited with value 1 indicating failure.
FAILED!

glam2:

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

  File "/home/matwright/Documents/meme-5.0.5/src/glam2html", line 43
    alen = 4
           ^
TabError: inconsistent use of tabs and spaces in indentation
Program glam2html exited with value 1
Warning: failed to convert output to HTML!
  File "/home/matwright/Documents/meme-5.0.5/src/glam2psfm", line 17
    print 'ALPHABET= ' + string.upper(''.join(letters))
                     ^
SyntaxError: invalid syntax
Program glam2psfm exited with value 1
Warning: failed to convert output to MEME format motif!
-------------------------------------------------------------------------------
glam2 exited with value 1 indicating failure.
FAILED!

glam2scan:

*******************************************************************************
Test glam2scan1 ...
glam2scan -O results/glam2scan1 p glam2/glam2.txt common/At.s &> log
Writing results to output directory 'results/glam2scan1'.
  File "/home/matwright/Documents/meme-5.0.5/src/glam2scan2html", line 24
    print '<html>'
                 ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print('<html>')?
Program glam2scan2html exited with value 1
Warning: failed to convert output to HTML!
-------------------------------------------------------------------------------
glam2scan exited with value 1 indicating failure.
FAILED!

 

[Matthew Wright]

Nevermind, I got it. It looked like I only had a python3 installation and was missing several perl modules (File::Which, HTML::Template, JSON). After installing those and all optional perl modules (Log::Log4perl, Math::CDF XML::Compile::SOAP11, XML::Compile::WSDL11) with cpan, make test was successful.

[Kristen Beck]

I actually have the same issue when trying to run glam2:

File "/Users/kristenbeck/miniconda3/libexec/meme-5.1.0/glam2html", line 43

    alen = 4

           ^

TabError: inconsistent use of tabs and spaces in indentation

Program glam2html exited with value 1

Warning: failed to convert output to HTML!

  File "/Users/kristenbeck/miniconda3/libexec/meme-5.1.0/glam2psfm", line 17

[Kristen Beck]

My install was via conda. On further investigation, it looks like the conda install pointed everything to the python 2.7 scripts instead of the python3 scripts. I will re-install via the tarball and compile. Hopefully, the issues will go away.

[Kristen Beck]

Posting in case it helps others... installing and compiling from tarball worked just fine. 

[Karan Bedi]

Hi Kristen,

Did you reinstall and compile using Python 2.7 instead of Python3?

Karan