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Pushya Krishna
Aug 16, 2019, 1:41:05 PM8/16/19
to MEME Suite Q&A
I tried installing meme-suite 5.0.5 and ran the make test command. My output showed that the test failed or skipped all of the tests. When I continue on to make install, all of the meme tests work (meme, meme-chip, mast, fimo, spamo etc.) however none of the motif format utilities are found (meme2meme, jaspar2meme etc.) I essentially have two questions. Why are all of the tests skipping and failing and how can I get meme2meme and the other motif format utilities to work? Does anyone have a solution or an answer for these?
OS: Windows 10, installed through linux subsystem (Ubuntu version: 1804.2019.521.0)
Here is my make test output:
pushyakrishna@DESKTOP-SFVPKU2:/mnt/c/Users/Pushya Krishna/meme-5.0.5$ make test
cd tests/scripts; make check
make[1]: Entering directory '/mnt/c/Users/Pushya Krishna/meme-5.0.5/tests/scripts'
make test_driver
make[2]: Entering directory '/mnt/c/Users/Pushya Krishna/meme-5.0.5/tests/scripts'
/bin/sed -e 's%@WHICHPERL@%/usr/bin/perl%' \
-e 's%@MYDISTDIR@%../..%' \
-e 's%@BUILDDIR@%../..%' \
-e 's%@TESTDIR@%../..%' test_driver.pl.in > test_driver
chmod +x test_driver
make[2]: Leaving directory '/mnt/c/Users/Pushya Krishna/meme-5.0.5/tests/scripts'
make check-TESTS
make[2]: Entering directory '/mnt/c/Users/Pushya Krishna/meme-5.0.5/tests/scripts'
make[3]: Entering directory '/mnt/c/Users/Pushya Krishna/meme-5.0.5/tests/scripts'
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)
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)
FAIL: ama1 (CRASH!)
FAIL: ama2 (CRASH!)
FAIL: ame1 (CRASH!)
FAIL: ame2 (CRASH!)
FAIL: ame3 (CRASH!)
FAIL: ame4 (CRASH!)
FAIL: ame5 (CRASH!)
FAIL: ame6 (CRASH!)
FAIL: ame7 (CRASH!)
FAIL: ame8 (CRASH!)
FAIL: ame9 (CRASH!)
FAIL: ame10 (CRASH!)
FAIL: ame11 (CRASH!)
FAIL: ame12 (CRASH!)
FAIL: ame13 (CRASH!)
FAIL: centrimo1 (CRASH!)
FAIL: centrimo2 (CRASH!)
FAIL: centrimo3 (CRASH!)
FAIL: centrimo4 (CRASH!)
FAIL: centrimo5 (CRASH!)
FAIL: centrimo6 (CRASH!)
FAIL: centrimo7 (CRASH!)
FAIL: centrimo8 (CRASH!)
FAIL: centrimo9 (CRASH!)
SKIP: cismapper1
SKIP: cismapper2
FAIL: create-priors1 (CRASH!)
FAIL: create-priors2 (CRASH!)
FAIL: dreme1 (CRASH!)
FAIL: dreme2 (CRASH!)
FAIL: dreme3 (CRASH!)
FAIL: dreme4 (CRASH!)
FAIL: fasta-center1 (CRASH!)
FAIL: fasta-dinucleotide-shuffle1 (CRASH!)
FAIL: fimo1 (CRASH!)
FAIL: fimo2 (CRASH!)
FAIL: fimo3 (CRASH!)
FAIL: fimo4 (CRASH!)
FAIL: glam2_1 (CRASH!)
FAIL: glam2scan1 (CRASH!)
FAIL: gomo1 (CRASH!)
FAIL: gomo2 (CRASH!)
FAIL: mast1 (CRASH!)
FAIL: mast2 (CRASH!)
FAIL: mast3 (CRASH!)
FAIL: mast4 (CRASH!)
FAIL: mast5 (CRASH!)
FAIL: mast6 (CRASH!)
FAIL: mast7 (CRASH!)
FAIL: mast8 (CRASH!)
FAIL: mast9 (CRASH!)
FAIL: mast10 (CRASH!)
FAIL: mast11 (CRASH!)
FAIL: mast12 (CRASH!)
FAIL: mast13 (CRASH!)
FAIL: mast14 (CRASH!)
FAIL: mast15 (CRASH!)
FAIL: mast16 (CRASH!)
FAIL: mast17 (CRASH!)
FAIL: mast18 (CRASH!)
FAIL: mast19 (CRASH!)
FAIL: mast20 (CRASH!)
FAIL: mast21 (CRASH!)
FAIL: mcast1 (CRASH!)
FAIL: mcast2 (CRASH!)
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!)
FAIL: meme-chip1 (CRASH!)
FAIL: momo1 (CRASH!)
FAIL: momo2 (CRASH!)
FAIL: momo3 (CRASH!)
FAIL: momo4 (CRASH!)
FAIL: momo5 (CRASH!)
FAIL: momo6 (CRASH!)
FAIL: momo7 (CRASH!)
FAIL: momo8 (CRASH!)
FAIL: momo9 (CRASH!)
FAIL: momo10 (CRASH!)
FAIL: momo11 (CRASH!)
FAIL: momo12 (CRASH!)
FAIL: momo13 (CRASH!)
FAIL: momo14 (CRASH!)
FAIL: momo15 (CRASH!)
FAIL: momo16 (CRASH!)
FAIL: momo17 (CRASH!)
FAIL: momo18 (CRASH!)
FAIL: motiph1 (CRASH!)
FAIL: motiph2 (CRASH!)
FAIL: psp-gen1 (CRASH!)
FAIL: psp-gen2 (CRASH!)
FAIL: psp-gen3 (CRASH!)
FAIL: qvalue1 (CRASH!)
FAIL: qvalue2 (CRASH!)
FAIL: spamo1 (CRASH!)
FAIL: spamo2 (CRASH!)
FAIL: spamo3 (CRASH!)
FAIL: spamo4 (CRASH!)
FAIL: tomtom1 (CRASH!)
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 5.0.5
============================================================================
# TOTAL: 150
# PASS: 0
# SKIP: 23
# XFAIL: 0
# FAIL: 127
# XPASS: 0
# ERROR: 0
============================================================================
See tests/scripts/test-suite.log
============================================================================
Here is my example of meme2meme not working:
pushyakrishna@DESKTOP-SFVPKU2:/mnt/c/Users/Pushya Krishna/meme-5.0.5$ meme-chip
Log::Log4perl configuration looks suspicious: No loggers defined at /usr/local/share/perl/5.26.1/Log/Log4perl/Config.pm line 325.
No sequences provided.
Usage:
meme-chip [options] [-db <motif file>]* <primary sequence file>
Options:
-o <dir> : output to the specified directory, failing if the directory exists
-oc <dir> : output to the specified directory, overwriting if the directory exists
-db <path> : target database for use by Tomtom and CentriMo; if not present,
Tomtom and CentriMo are not run
-neg <path> : negative (control) sequence file name;
the control sequences will be input to MEME, CentriMo and DREME,
and MEME will use the Differential Enrichment objective function;
sequences are assumed to originate from the same alphabet as the
primary sequence file and should be the same length as those;
default: no negative sequences are used for MEME
or CentriMo, and for DREME, the primary sequences
are shuffled to create the negative set
-psp-gen use the psp-gen program to create a position-specific
prior for use by MEME with its Classic objective function;
requires -neg; default: input control sequences directly
to MEME and use its Differential Enrichment objective function
-dna set the alphabet to DNA; this is the default
-rna set the alphabet to RNA
-[x]alph <path> : alphabet file; when the x is specified the motif
databases are converted to the specified alphabet;
default: DNA
-bfile <path> : background file
-order <ord> : set the order of the Markov background model
that is generated from the sequences when a
background file is not given; default: 1
-seed <seed> : seed for the randomized selection of sequences
for MEME and the shuffling of sequences for DREME;
default: seed randomly
-ccut <num> : maximum size of a sequence before it is cut down
to a centered section; a value of 0 indicates the
sequences should not be cut down; default: 100
-group-thresh <gthr> : primary threshold for clustering motifs; default: 0.05
-group-weak <gwk> : secondary threshold for clustering motifs; default: 2*gthr
-filter-thresh <fthr> : E-value threshold for including motifs; default: 0.05
-time <minutes> : maximum time that this program has to run and
create output in; default: no limit
-desc <text> : description of the job
-fdesc <file> : file containing plain text description of the job
-norc : search given strand only
-old-clustering : pick cluster seed motifs based only on significance;
default: preferentially select discovered motifs as
clustering seeds even if there is a library motif
that appears more enriched
-noecho : don't echo the commands run
-help : display this help message
-version : print the version and exit
MEME Specific Options:
-meme-brief <num> : reduce size of MEME output files if more than <num>
: primary sequences
-meme-mod [oops|zoops|anr]: sites used in a single sequence
-meme-minw <num> : minimum motif width
-meme-maxw <num> : maximum motif width
-meme-nmotifs <num> : maximum number of motifs to find
-meme-minsites <num> : minimum number of sites per motif
-meme-maxsites <num> : maximum number of sites per motif
-meme-p <np> : use parallel version with <np> processors
-meme-pal : look for palindromes only
-meme-searchsize <num> : the maximum portion of the primary sequences (in characters)
: used for motif search; MEME's running time increases as
: roughly the square of <num>
-meme-nrand : MEME should not randomize sequence order
DREME Specific Options:
-dreme-e <num> : stop searching after reaching this E-value threshold
-dreme-m <num> : stop searching after finding this many motifs
CentriMo Specific Options:
-centrimo-local : compute enrichment of all regions (not only central)
-centrimo-score <num> : set the minimum allowed match score
-centrimo-maxreg <num> : set the maximum region size to be considered
-centrimo-ethresh <num> : set the E-value threshold for reporting
-centrimo-noseq : don't store sequence IDs in the output
-centrimo-flip : reflect matches on reverse strand around center
SpaMo Specific Options:
-spamo-skip : don't run SpaMo
FIMO Specific Options:
-fimo-skip : don't run FIMO
pushyakrishna@DESKTOP-SFVPKU2:/mnt/c/Users/Pushya Krishna/meme-5.0.5$ meme2meme
meme2meme: command not found
Please let me know if you have any answers or if there is any information I can provide to clarify anything.
Thanks!
cegrant
Aug 20, 2019, 6:45:57 PM8/20/19
to MEME Suite Q&A
how can I get meme2meme and the other motif format utilities to work?
Users had pointed out to us that by putting all the supporting scripts and utilities in the ‘bin’ directory we were creating potential naming collisions, so the MEME Suite installation now puts the supporting scripts and utilities in libexec/meme-X.Y.Z, where X.Y.Z is the version number of the release. If you want to use the scripts without typing the full path you’ll need to add the libexec/meme-X.Y.Z directory to your execution PATH. This is discussed in the installation guide, at “Step 5” of the section “Installing from a tarball”.
Why are all of the tests skipping and failing
I can't say from the information you've posted here. If you look in the directory tests/scripts there should be a log file for the test of each component. The log file should contain more information about why the test failed.
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