FAIL: meme1 (CRASH!) and FAIL: tomtom_allr (CRASH!)

[JLSunday]

Hi everyone,

I'm trying to install the meme suite of according the QUICK INSTALL ...

The problem appears in the part meme and tomton when i write MAKE TEST ...

Sundays-Macbook-Pro:meme_4.11.2 JLSunday$ make test

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%' test_driver.pl.in > test_driver

chmod +x test_driver

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

PASS: ama1

PASS: ama2

PASS: ame1

PASS: centrimo1

PASS: create-priors1

PASS: create-priors2

PASS: dreme1

PASS: dreme2

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

FAIL: meme1 (CRASH!)

FAIL: meme2 (CRASH!)

FAIL: meme3 (CRASH!)

FAIL: meme4 (CRASH!)

FAIL: meme5 (CRASH!)

FAIL: meme6 (CRASH!)

PASS: meme_psp

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)

SKIP: motif-in.dreme.klf1.text (dreme.txt missing)

PASS: motif-in.dreme.klf1.xml

SKIP: motif-in.dreme.klf1.html (dreme.html missing)

SKIP: motif-in.dreme.klf1.extdna.text (dreme.txt missing)

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

SKIP: motif-in.dreme.klf1.extdna.html (dreme.html missing)

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

PASS: motif-in.dreme.puf3p.xml

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: spamo1

PASS: spamo2

FAIL: tomtom_allr (CRASH!)

FAIL: tomtom_ed (CRASH!)

FAIL: tomtom_kullback (CRASH!)

FAIL: tomtom_pearson (CRASH!)

FAIL: tomtom_sandelin (CRASH!)

FAIL: tomtom_blic1 (CRASH!)

FAIL: tomtom_blic5 (CRASH!)

FAIL: tomtom_allr_cs (CRASH!)

FAIL: tomtom_ed_cs (CRASH!)

FAIL: tomtom_kullback_cs (CRASH!)

FAIL: tomtom_pearson_cs (CRASH!)

FAIL: tomtom_sandelin_cs (CRASH!)

FAIL: tomtom_blic1_cs (CRASH!)

FAIL: tomtom_blic5_cs (CRASH!)

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

Testsuite summary for meme 4.11.2

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

# TOTAL: 87

# PASS:  49

# SKIP:  18

# XFAIL: 0

# FAIL:  20

# 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

I hope your help...

Regards

[CharlesEGrant]

Do you have all the required Perl modules installed? Check the section on Perl prerequisites in the installation guide.

[JLSunday]

Hi again,

 

Happy New Year!

 

Thanks for you answer my question. I installed the MEME Suite without "error". Only I could not install a file of perl ... HTML::Template... but MEME Suite was installed.

 

However, When I run the meme for to get logos appears an error.

 

Sundays-Macbook-Pro:~ JLSunday$ meme /Users/JLSunday/Desktop/CTLs/2.-\ CTLs.fasta -protein -nmotifs 5 -mod oops -minw 10 -maxw 50 -maxsize 10000

The output directory 'meme_out' already exists.

Its contents will be overwritten.

 

Illegal character `-' in sequence ath|Arabidopsis_thaliana_AT4G00070.1_CTL15.

Change alphabet or fix data file.

[CharlesEGrant]

HTML::Template is required for MEME and several other tools in the MEME Suite to work correctly. When you ran 'configure' there should have been a warning message about missing required Perl modules. If modules are missing MEME may install,  but it will fail when MEME tries to write out the results in HTML format. 

The other error 

Illegal character `-' in sequence ath|Arabidopsis_thaliana_AT4G00070.1_CTL15.

 

is unrelated. That seems to indicate that you sequence data contains gaps. The FASTA files provided to MEME are limited to amino acids and ambiguity codes. They can't contain gaps. The standard alphabets supported by MEME are described here: http://meme-suite.org/doc/alphabets.html#protein 

[boyas...@gmail.com]

thanks for your sharing, Sunday.

would you mind telling me How can I solve the problem listed above?

Although I installed Math::CDF module, I encounter with the following warnings

Testsuite summary for meme 4.11.3 ============================================================================ # TOTAL: 87 # PASS: 45 # SKIP: 18 # XFAIL: 0 # FAIL: 24 including FAIL: fasta-center1 (CRASH!)

# XPASS: 0 # ERROR: 0

Yes, Math::CDF is Only required for fasta-enriched-center script. But I want to analyze the fasta files using meme.

Thanks for your help.

[boyas...@gmail.com]

Thanks for your kindness.

How can I tackle the warning when processing 1000 kb fasta file:

Dataset too large (> 100000).  Rerun with larger -maxsize.

In addition, how to choose the proper utility of meme when comparing two fasta files, such as human promoters VS. mouse promoters of genes in the same family.

Sorry to occupying your precious time.

[CharlesEGrant]

How can I tackle the warning when processing 1000 kb fasta file:
Dataset too large (> 100000).  Rerun with larger -maxsize.

This is described in the documentation for the command line version of MEME.

Check the description of the -maxsize option.

In addition, how to choose the proper utility of meme when comparing two fasta files, such as human promoters VS. mouse promoters of genes in the same family.

As indicated on the MEME Suite home page, TomTom is the MEME Suite tool for comparing motifs.

By the way, these questions aren't related to the other items in this thread. Please start a new thread if you are asking an unrelated question. 

[CharlesEGrant]

would you mind telling me How can I solve the problem listed above?
Although I installed Math::CDF module, I encounter with the following warnings
Testsuite summary for meme 4.11.3

I suspect you are missing some of the required Perl modules, or the required versions of Python and Perl. Did you see any error messages when you ran 'configure' or 'make'?

Try running 

cd scripts 

perl dependencies.pl

This should list the Perl modules you need to install.

Also, look in the directory tests/scripts. There should be a log file for each of the tests. The failing tests should have more information about what caused them to fail.