MEME 5.5.5 XSTREME CRASH

[Mayur Kedare]

Hi,

Has anyone encountered xstreme fail when you do make check? If you do what do you do for it to work? I have used the previous version and it was working fine in my own PC and it was slow so I tried to install in HPC and this time
I have tried to run the latest version on HPC cluster but it stalled and didn't give output.

I have installed MEME on HPC cluster. With basic installation as per manual.
tar zxf meme-5.5.5.tar.gz cd meme-5.5.5 ./configure --prefix=$HOME/meme --enable-build-libxml2 --enable-build-libxslt make make test make install

Here is the relevant information for you to consider.
the MEME Suite version:
5.5.5
the OS version:
Linux version 3.10.0-1062.el7.x86_64 (mock...@kbuilder.bsys.centos.org) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-36) (GCC) ) #1 SMP Wed Aug 7 18:08:02 UTC 2019
the autoconf version:
autoconf (GNU Autoconf) 2.69
the compiler version:
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-39)
the Perl version:
perl 5, version 16, subversion 3 (v5.16.3) built for x86_64-linux-thread-multi
(with 39 registered patches, see perl -V for more detail)
the Python version:
Python 2.7.5
the python3 version:
Python 3.6.8

I have pasted test.log here:

r@cpu-login2 meme-5.5.5]$ cat test.log
make check
make[1]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5'
make  check-recursive
make[2]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5'
Making check in etc
make[3]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/etc'
make[3]: Nothing to be done for `check'.
make[3]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/etc'
Making check in src
make[3]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/src'
make  check-recursive
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/src'
Making check in filters
make[5]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/src/filters'
Making check in purge
make[6]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/src/filters/purge'
make[6]: Nothing to be done for `check'.
make[6]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/src/filters/purge'
Making check in dust
make[6]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/src/filters/dust'
make[6]: Nothing to be done for `check'.
make[6]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/src/filters/dust'
make[6]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/src/filters'
make[6]: Nothing to be done for `check-am'.
make[6]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/src/filters'
make[5]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/src/filters'
Making check in libxml2
make[5]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/src/libxml2'
Making check in include
make[6]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/src/libxml2/include'
Making check in .
make[7]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/src/libxml2/include'
make[7]: Nothing to be done for `check-am'.
make[7]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/src/libxml2/include'
Making check in libxml
make[7]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/src/libxml2/include/libxml'
make[7]: Nothing to be done for `check'.
make[7]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/src/libxml2/include/libxml'
make[6]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/src/libxml2/include'
Making check in .
make[6]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/src/libxml2'
make[6]: Nothing to be done for `check-am'.
make[6]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/src/libxml2'
make[5]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/src/libxml2'
Making check in libxslt
make[5]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/src/libxslt'
make[5]: Nothing to be done for `check'.
make[5]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/src/libxslt'
Making check in .
make[5]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/src'
make[5]: Nothing to be done for `check-am'.
make[5]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/src'
Making check in parallel
make[5]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/src/parallel'
cp -f meme ../meme;
make[5]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/src/parallel'
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/src'
make[3]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/src'
Making check in scripts
make[3]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/scripts'
make[3]: Nothing to be done for `check'.
make[3]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/scripts'
Making check in tests
make[3]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests'
Making check in ame
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/ame'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/ame'
Making check in bed2fasta
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/bed2fasta'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/bed2fasta'
Making check in clustalw2fasta
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/clustalw2fasta'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/clustalw2fasta'
Making check in centrimo
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/centrimo'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/centrimo'
Making check in common
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/common'
Making check in motif.crp0
make[5]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/common/motif.crp0'
make[5]: Nothing to be done for `check'.
make[5]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/common/motif.crp0'
Making check in motif.Puf3p
make[5]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/common/motif.Puf3p'
make[5]: Nothing to be done for `check'.
make[5]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/common/motif.Puf3p'
make[5]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/common'
make  Klf1-200-100-shuffled.fa
make[6]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/common'
make[6]: `Klf1-200-100-shuffled.fa' is up to date.
make[6]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/common'
make[5]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/common'
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/common'
Making check in create-priors
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/create-priors'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/create-priors'
Making check in draw-mhmm
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/draw-mhmm'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/draw-mhmm'
Making check in dreme
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/dreme'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/dreme'
Making check in fasta-center
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/fasta-center'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/fasta-center'
Making check in fimo
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/fimo'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/fimo'
Making check in glam2
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/glam2'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/glam2'
Making check in glam2scan
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/glam2scan'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/glam2scan'
Making check in gomo
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/gomo'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/gomo'
Making check in mast
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/mast'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/mast'
Making check in mcast
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/mcast'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/mcast'
Making check in meme
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/meme'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/meme'
Making check in meme-chip
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/meme-chip'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/meme-chip'
Making check in mhmm
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/mhmm'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/mhmm'
Making check in mhmms
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/mhmms'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/mhmms'
Making check in momo
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/momo'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/momo'
Making check in mhmmscan
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/mhmmscan'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/mhmmscan'
Making check in motiph
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/motiph'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/motiph'
Making check in psp-gen
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/psp-gen'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/psp-gen'
Making check in qvalue
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/qvalue'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/qvalue'
Making check in scaffold
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/scaffold'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/scaffold'
Making check in sea
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/sea'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/sea'
Making check in spamo
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/spamo'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/spamo'
Making check in streme
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/streme'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/streme'
Making check in tgene
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/tgene'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/tgene'
Making check in tomtom
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/tomtom'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/tomtom'
Making check in web
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/web'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/web'
Making check in xstreme
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/xstreme'
make[4]: Nothing to be done for `check'.
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/xstreme'
Making check in scripts
make[4]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/scripts'
make  test_driver
make[5]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/scripts'
make[5]: `test_driver' is up to date.
make[5]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/scripts'
make  check-TESTS
make[5]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/scripts'
make[6]: Entering directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/scripts'
PASS: bed2fasta1
PASS: bed2fasta2
PASS: bed2fasta3
PASS: bed2fasta4
PASS: bed2fasta5
PASS: bed2fasta6
PASS: bed2fasta7
PASS: bed2fasta8
PASS: bed2fasta9
PASS: bed2fasta10
PASS: bed2fasta11
PASS: bed2fasta12
PASS: motif-in.streme.klf1.text
PASS: motif-in.streme.klf1.xml
PASS: motif-in.streme.klf1.html
PASS: motif-in.streme.klf1.extdna.text
PASS: motif-in.streme.klf1.extdna.xml
PASS: motif-in.streme.klf1.extdna.html
PASS: motif-in.streme.puf3p.text
PASS: motif-in.streme.puf3p.xml
PASS: motif-in.streme.puf3p.html
PASS: motif-in.streme.lipocalin.text
PASS: motif-in.streme.lipocalin.xml
PASS: motif-in.streme.lipocalin.html
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: 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: tgene1
PASS: tgene2
PASS: tgene3
PASS: tgene4
PASS: create-priors1
PASS: create-priors2
ERROR: /home/stud/tgangar/MEME/meme-5.5.5/tests/scripts/dreme.test (FAULT IN TEST!)
PASS: fasta-center1
PASS: fimo1
PASS: fimo2
PASS: fimo3
PASS: fimo4
PASS: fimo5
PASS: fimo6
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
PASS: meme1
PASS: meme2
PASS: meme3
PASS: meme4
PASS: meme5
PASS: meme6
PASS: meme7
PASS: meme8
PASS: meme9
PASS: meme10
PASS: meme11
PASS: meme12
PASS: meme13
PASS: meme14
PASS: meme15
PASS: meme16
PASS: meme17
PASS: meme18
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: momo18
PASS: motiph1
PASS: motiph2
PASS: psp-gen1
PASS: psp-gen2
PASS: psp-gen3
PASS: qvalue1
PASS: qvalue2
PASS: sea1
PASS: sea2
PASS: sea3
PASS: sea4
PASS: spamo1
PASS: spamo2
PASS: spamo3
PASS: spamo4
PASS: spamo5
PASS: spamo6
PASS: streme1
PASS: streme2
PASS: streme3
PASS: streme4
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
FAIL: xstreme1 (CRASH!)
FAIL: xstreme2 (CRASH!)
FAIL: xstreme3 (CRASH!)
FAIL: xstreme4 (CRASH!)
FAIL: xstreme5 (CRASH!)
PASS: fasta-dinucleotide-shuffle1
============================================================================
Testsuite summary for meme 5.5.5
============================================================================
# TOTAL: 190
# PASS:  183
# SKIP:  0
# XFAIL: 0
# FAIL:  6
# XPASS: 0
# ERROR: 1
============================================================================
See tests/scripts/test-suite.log
============================================================================
make[6]: *** [test-suite.log] Error 1
make[6]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/scripts'
make[5]: *** [check-TESTS] Error 2
make[5]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/scripts'
make[4]: *** [check-am] Error 2
make[4]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests/scripts'
make[3]: *** [check-recursive] Error 1
make[3]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5/tests'
make[2]: *** [check-recursive] Error 1
make[2]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5'
make[1]: *** [check] Error 2
make[1]: Leaving directory `/home/stud/tgangar/MEME/meme-5.5.5'
make: *** [test] Error 2



cat xstreme.log
*******************************************************************************
Test xstreme1 ...
xstreme --p common/crp0.s --oc results/xstreme1 --verbosity 0 --m meme-chip/JASPAR_CORE_2014_vertebrates.meme --minw 16 --maxw 20 &> log
Can't locate XML/Simple.pm in @INC (@INC contains: /home/stud/tgangar/MEME/meme-5.5.5/scripts /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/stud/tgangar/MEME/meme-5.5.5/scripts/xstreme line 136.
BEGIN failed--compilation aborted at /home/stud/tgangar/MEME/meme-5.5.5/scripts/xstreme line 136.
-------------------------------------------------------------------------------
xstreme exited with value 2 indicating failure.
FAILED!
*******************************************************************************
Test xstreme2 ...
xstreme --p common/adh.s --oc results/xstreme2 --verbosity 0 --protein &> log
Can't locate XML/Simple.pm in @INC (@INC contains: /home/stud/tgangar/MEME/meme-5.5.5/scripts /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/stud/tgangar/MEME/meme-5.5.5/scripts/xstreme line 136.
BEGIN failed--compilation aborted at /home/stud/tgangar/MEME/meme-5.5.5/scripts/xstreme line 136.
-------------------------------------------------------------------------------
xstreme exited with value 2 indicating failure.
FAILED!
*******************************************************************************
Test xstreme3 ...
xstreme --p common/Puf3p-200.s --oc results/xstreme3 --verbosity 0 --rna --evt 0.5 --meme-evt 0.05 --streme-evt 0.2 &> log
Can't locate XML/Simple.pm in @INC (@INC contains: /home/stud/tgangar/MEME/meme-5.5.5/scripts /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/stud/tgangar/MEME/meme-5.5.5/scripts/xstreme line 136.
BEGIN failed--compilation aborted at /home/stud/tgangar/MEME/meme-5.5.5/scripts/xstreme line 136.
-------------------------------------------------------------------------------
xstreme exited with value 2 indicating failure.
FAILED!
*******************************************************************************
Test xstreme4 ...
xstreme --p common/dna_with_covalent.fa --oc results/xstreme4 --verbosity 0 --m common/Jaspar-subset.meme --m common/dna_with_covalent.meme --meme-nmotifs 3 --streme-nmotifs 2 --meme-searchsize 10000 --xalph common/dna_with_covalent.alph --bfile common/dna_with_covalent.bg --ctrim 100 &> log
Can't locate XML/Simple.pm in @INC (@INC contains: /home/stud/tgangar/MEME/meme-5.5.5/scripts /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/stud/tgangar/MEME/meme-5.5.5/scripts/xstreme line 136.
BEGIN failed--compilation aborted at /home/stud/tgangar/MEME/meme-5.5.5/scripts/xstreme line 136.
-------------------------------------------------------------------------------
xstreme exited with value 2 indicating failure.
FAILED!
*******************************************************************************
Test xstreme5 ...
xstreme --p common/nrmix.100bp.fa --oc results/xstreme5 --verbosity 0 --m meme-chip/JASPAR_CORE_2014_vertebrates.meme --mea-only &> log
Can't locate XML/Simple.pm in @INC (@INC contains: /home/stud/tgangar/MEME/meme-5.5.5/scripts /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /home/stud/tgangar/MEME/meme-5.5.5/scripts/xstreme line 136.
BEGIN failed--compilation aborted at /home/stud/tgangar/MEME/meme-5.5.5/scripts/xstreme line 136.
-------------------------------------------------------------------------------
xstreme exited with value 2 indicating failure.
FAILED!

[cegrant]

Hi, the MEME Suite depends on several Perl modules that may or may not be pre-installed on your system. If you look at the messages explaining the test failure for xstreme at the end your log you'll note that they all complain that the Perl module XML/Simple.pm can't be found. You'll need to install the module XML::Simple on  your system.

Be sure to read the section on prerequisite software in the MEME Suite installation guide. In particular, the section on Perl requirements will explain how to check  your system to see if the required Perl modules are installed, and how to install them if they are missing.

As an alternative to building the MEME Suite from source you may want to consider installing Docker and using the MEME Suite Docker image.

[Mayur Kedare]

Hi @cegrant Thank you for your reply. I moved to HPC because XSTREME was slow for finding motif with my dataset and I used Docker to install in my own computer. It was stalling in old as well as new version. I also tried with the same data only it was DNA sequence of the proteins and it gave output fairly in expected time albeit slow and I can expect it to be that way because xstreme is performing several task. I will also ask HPC admin to install prerequisite softwares and perl dependencies or use by Docker, as I don't have access to install in other directories. Can the installation on HPC be done through Singularity?

[cegrant]

What part of XSTREME seemed to be hanging? If all you need to do is de novo detection of motifs then you might consider running MEME or STREME by themselves rather than XSTREME. Note that MEME is the only component of the MEME Suite that is parallelized. Putting the MEME Suite on a cluster won't improve the speed of any of the other tools. A system with more RAM might help, but we'd need to know which tools is the bottleneck to advise on that.

What is the size and nature of your input data? Note that MEME will downsample the input sequences if there are more than 1000 sequences, so be aware that simply throwing more sequences at MEME will not improve the results.

We have no experience with Singularity, but their documentation indicates that it can use Docker images.