make check failed in meme@5.3.0

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xijun shi

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Mar 29, 2021, 5:19:22 AM3/29/21

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[root@centos8 spack-src]# make check

make check-recursive

make[1]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src'

Making check in src

make[2]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src'

make check-recursive

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src'

Making check in filters

make[4]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/filters'

Making check in purge

make[5]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/filters/purge'

make[5]: Nothing to be done for 'check'.

make[5]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/filters/purge'

Making check in dust

make[5]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/filters/dust'

make[5]: Nothing to be done for 'check'.

make[5]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/filters/dust'

make[5]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/filters'

make[5]: Nothing to be done for 'check-am'.

make[5]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/filters'

make[4]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/filters'

Making check in libxml2

make[4]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/libxml2'

Making check in include

make[5]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/libxml2/include'

Making check in .

make[6]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/libxml2/include'

make[6]: Nothing to be done for 'check-am'.

make[6]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/libxml2/include'

Making check in libxml

make[6]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/libxml2/include/libxml'

make[6]: Nothing to be done for 'check'.

make[6]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/libxml2/include/libxml'

make[5]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/libxml2/include'

Making check in .

make[5]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/libxml2'

make[5]: Nothing to be done for 'check-am'.

make[5]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/libxml2'

make[4]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/libxml2'

Making check in libxslt

make[4]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/libxslt'

make[4]: Nothing to be done for 'check'.

make[4]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/libxslt'

Making check in .

make[4]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src'

make[4]: Nothing to be done for 'check-am'.

make[4]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src'

Making check in parallel

make[4]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/parallel'

cp -f meme ../meme;

make[4]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src/parallel'

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src'

make[2]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/src'

Making check in scripts

make[2]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/scripts'

make[2]: Nothing to be done for 'check'.

make[2]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/scripts'

Making check in tests

make[2]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests'

Making check in ame

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/ame'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/ame'

Making check in clustalw2fasta

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/clustalw2fasta'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/clustalw2fasta'

Making check in centrimo

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/centrimo'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/centrimo'

Making check in common

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/common'

Making check in motif.crp0

make[4]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/common/motif.crp0'

make[4]: Nothing to be done for 'check'.

make[4]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/common/motif.crp0'

Making check in motif.Puf3p

make[4]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/common/motif.Puf3p'

make[4]: Nothing to be done for 'check'.

make[4]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/common/motif.Puf3p'

make[4]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/common'

make Klf1-200-100-shuffled.fa

make[5]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/common'

cp Klf1-200-100-shuffled.py3.fa ../../tests/common/Klf1-200-100-shuffled.fa

make[5]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/common'

make[4]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/common'

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/common'

Making check in create-priors

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/create-priors'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/create-priors'

Making check in draw-mhmm

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/draw-mhmm'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/draw-mhmm'

Making check in dreme

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/dreme'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/dreme'

Making check in fasta-center

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/fasta-center'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/fasta-center'

Making check in fimo

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/fimo'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/fimo'

Making check in glam2

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/glam2'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/glam2'

Making check in glam2scan

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/glam2scan'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/glam2scan'

Making check in gomo

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/gomo'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/gomo'

Making check in mast

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/mast'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/mast'

Making check in mcast

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/mcast'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/mcast'

Making check in meme

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/meme'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/meme'

Making check in meme-chip

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/meme-chip'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/meme-chip'

Making check in mhmm

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/mhmm'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/mhmm'

Making check in mhmms

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/mhmms'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/mhmms'

Making check in momo

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/momo'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/momo'

Making check in mhmmscan

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/mhmmscan'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/mhmmscan'

Making check in motiph

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/motiph'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/motiph'

Making check in psp-gen

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/psp-gen'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/psp-gen'

Making check in qvalue

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/qvalue'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/qvalue'

Making check in scaffold

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/scaffold'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/scaffold'

Making check in spamo

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/spamo'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/spamo'

Making check in streme

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/streme'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/streme'

Making check in tgene

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/tgene'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/tgene'

Making check in tomtom

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/tomtom'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/tomtom'

Making check in web

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/web'

make[3]: Nothing to be done for 'check'.

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/web'

Making check in scripts

make[3]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/scripts'

make test_driver

make[4]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/scripts'

/usr/bin/sed -e 's%@WHICHPERL@%/home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-5.32.1-3cibemokw65lgp7rvf7wrkelypdl72z5/bin/perl%' \

-e 's%@MYDISTDIR@%/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src%' \

-e 's%@BUILDDIR@%/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src%' \

-e 's%@TESTDIR@%/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src%' test_driver.pl.in > test_driver

chmod +x test_driver

make[4]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/scripts'

make check-TESTS

make[4]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/scripts'

make[5]: Entering directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/scripts'

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: /tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/scripts/dreme.test (FAULT IN TEST!)

PASS: fasta-center1

FAIL: fasta-dinucleotide-shuffle1 (differences in stdout)

PASS: fimo1

FAIL: fimo2 (differences in fimo.tsv)

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: 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: spamo1

PASS: spamo2

PASS: spamo3

PASS: spamo4

PASS: streme1

PASS: streme2

PASS: streme3

PASS: streme4

PASS: tomtom1

PASS: tomtom_allr

PASS: tomtom_ed

PASS: tomtom_kullback

FAIL: tomtom_pearson (differences in tomtom.html)

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 5.3.0

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

# TOTAL: 165

# PASS: 160

# SKIP: 0

# XFAIL: 0

# FAIL: 4

# XPASS: 0

# ERROR: 1

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

See tests/scripts/test-suite.log

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

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

Test fasta-dinucleotide-shuffle1 ...

fasta-dinucleotide-shuffle -f common/Klf1-200-100.fa -t -dinuc 1> results/fasta-dinucleotide-shuffle1/fasta-dinucleotide-shuffle_pHWN4_stdout 2> log

reference common/Klf1-200-100-shuffled.py2.fa output results/fasta-dinucleotide-shuffle1/fasta-dinucleotide-shuffle_pHWN4_stdout

-------------------------------------------------------------------------------

2c2

< AGCAAACCATCCACTAATACGCACTGTTGACTCTACTGATAGAATCTGCCTGAACGACCAAAGAACACTTCCAGCAATTCAGCACACCCATGAGACGCCA

---

> AAAGACCCTGACCACACACTGCTTGATGCCGAAGAAGCAAACTTTACCTACATGACTCTCGAATATCCACACCCATCACACTCAGCATAAAGCGAGTGCA

4c4

< AGCCCACCTGAATCAGGAGATACATAGATTGGAATGCTCTGAAGTGTCAAATGTCCCTCTCTGTTCCAGCACTTTTCTCTGAAGTAAGCCTTCCAACCTA

...

make[5]: *** [Makefile:591: test-suite.log] Error 1

make[5]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/scripts'

make[4]: *** [Makefile:699: check-TESTS] Error 2

make[4]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/scripts'

make[3]: *** [Makefile:766: check-am] Error 2

make[3]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/scripts'

make[2]: *** [Makefile:412: check-recursive] Error 1

make[2]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests'

make[1]: *** [Makefile:779: check-recursive] Error 1

make[1]: Leaving directory '/tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src'

make: *** [Makefile:1077: check] Error 2

[root@centos8 spack-src]# vim tests/scripts/test-suite.log

……

> AGTCCTGCCAGCAGGCTGCGGGGATCGTTGGAATCAGTTGGGGAGTTCCTCAGTGAGTTCCCGGTTGAGTCTTGCTGTTTTGTCTTCTTAGCCAGTAGCA

328c328

< GGTCACCCAGTATCTGAGCCACACACTGCCTGAGAGGAGCTCTGAGCACAGCACCGTCATTCATGAACACCTCCCAATATTAGCGACCTATGAGCCCGTG

---

> GCCTGCTCCGTCGACAGAGACAGGAGTGAGCAATTGCATCAGTATCGAGATGCTCCTGCCCCTTACCACCCATGACCTACTGTACACCATCAAGCACAGG

330c330

< TCATTTGAGCTAATGCCTGCGGTTGTGCGAATGATTTTTTCCCTTCAACCGCAAGTCCTCGTTCTATTCACTGTTTAGTAGCTGTCTGCGCTCTGGCAGA

---

> TAGATTTGCAGAAGTGCCCTCTTTTGCATAAGTCGCGCTGTTGATTCAGGGCTTCGCACCTTGCGATGTAAACATCTTCGTCCTTTTGTCTGTCTGCCTA

332c332

< GTTCAAGATGTTTTAGTGTGAGAAGGTATGTTTACACAGACCTCGAGCCGTGGCTCCCGTTTTTCAGGTCCGGCCCATATTAGTGGCCTCCAAAAAAGGT

---

> GTAAGTCAAATTTTCAGTGCATCCGTTGCATAAGAGTTAGAGTAACTCCCGCCCGACAGCAATTTTCCCCCTTGTCGGGAGGTTGTGGGGAACTGTTAGT

334c334

< GACCACTAAGCTTGCCATCAATTTGTTTCTAAGGAAGCCCCTTAAGGGAATTTTCTCCTTATGCTGAGAGGATTTAAATTTCCCTTCCTGGGGAGCTATC

---

> GGAAGCTAGGGCCCAACTTTTCCTTGGGCCCAATCCTTTATTCAGATAGGATTGAGCCTTCTTGGTCCTGCTTTAAATTGAGAACTTATTCTAGAAATCC

336c336

< TCTTGGAGTAGGGCTGGAAGTTGTGAGCCAGGCCGTGGTCTCTTGGACCTGTGGAGCCAAGCCTCCCTAACCACTCTCCTTGATTCTAGGGCTGCTTATT

---

> TCTCCTGTTTCTCCCCTTGTGGCTGGCCTCTACTGAGTAGTCCGGGTCAAGAAGACACTTTAGATGCTTGCCTGGGCCCAGTGAGGGCTGGCTTAGGAAT

338c338

< GATCATTTCAAGCCAAGGCTTCGGAGTGCAGGAACATGAAATGTGCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

---

> GAATGAAAGAGCAATCTCATTTGGTTGCACATCGTGAAAGGGCCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

FAILED!

……

Test fimo2 ...

fimo --oc results/fimo2 --motif CGGYGGGG --motif GCATCRGRBSAGA --no-qvalue --thresh 0.01 common/crp0.meme.xml /tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/motiph/spiked.fasta &> log

Skipping motif +TKTGANCNABNTCACAHWT.

Skipping motif -TKTGANCNABNTCACAHWT.

Using motif +CGGYGGGG of width 8.

Using motif -CGGYGGGG of width 8.

Using motif +GCATCRGRBSAGA of width 13.

Using motif -GCATCRGRBSAGA of width 13.

reference /tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/fimo/fimo-motif23.tsv output results/fimo2/fimo.tsv

-------------------------------------------------------------------------------

14d13

< CGGYGGGG MEME-2 Scer 2130 2137 + 2.51429 0.00441 0 CTTTGGGG

15a15

> CGGYGGGG MEME-2 Scer 2130 2137 + 2.51429 0.00441 0 CTTTGGGG

25,28d24

< CGGYGGGG MEME-2 Scer 226 233 + -2.71429 0.00808 0 CATAGGGG

< CGGYGGGG MEME-2 Scer 326 333 + -2.71429 0.00808 0 CGGAGCGT

< CGGYGGGG MEME-2 Scer 972 979 + -2.71429 0.00808 0 TGGAGTGG

< CGGYGGGG MEME-2 Scer 1696 1703 + -2.71429 0.00808 0 CTTAGGGG

33a30,33

> CGGYGGGG MEME-2 Scer 226 233 + -2.71429 0.00808 0 CATAGGGG

> CGGYGGGG MEME-2 Scer 326 333 + -2.71429 0.00808 0 CGGAGCGT

> CGGYGGGG MEME-2 Scer 972 979 + -2.71429 0.00808 0 TGGAGTGG

> CGGYGGGG MEME-2 Scer 1696 1703 + -2.71429 0.00808 0 CTTAGGGG

FAILED!

……

Test meme-chip1 ...

meme-chip -oc results/meme-chip1 -db meme-chip/JASPAR_CORE_2014_vertebrates.meme meme-chip/Klf1.100.fa &> log

Can't locate XML/Simple.pm in @INC (you may need to install the XML::Simple module) (@INC contains: /tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/scripts /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-xml-parser-2.44-mn2pedkdvm6ctbdhzshjx7m7vjtkkikj/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-xml-parser-2.44-mn2pedkdvm6ctbdhzshjx7m7vjtkkikj/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-libwww-perl-6.33-7rlrgce5grfd6ibbps2d43epwxrpszqc/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-libwww-perl-6.33-7rlrgce5grfd6ibbps2d43epwxrpszqc/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-encode-locale-1.05-kzfwuf6am2iuas6mty4ff25zizwzkgrc/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-encode-locale-1.05-kzfwuf6am2iuas6mty4ff25zizwzkgrc/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-file-listing-6.04-yt3kfxx2adgczim67wgdnd3nt626h4s7/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-file-listing-6.04-yt3kfxx2adgczim67wgdnd3nt626h4s7/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-http-date-6.02-3o5ui2o5nlyxi4dggz5cags47yglqiti/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-http-date-6.02-3o5ui2o5nlyxi4dggz5cags47yglqiti/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-html-parser-3.72-bojckdowuzbxqidqwqhr2lfegijyo3ue/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-html-parser-3.72-bojckdowuzbxqidqwqhr2lfegijyo3ue/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-html-tagset-3.20-hpf66do4ksavx46c4mwhnt7wllvpynhx/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-html-tagset-3.20-hpf66do4ksavx46c4mwhnt7wllvpynhx/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-http-cookies-6.04-7kzsef2amsex5oidodbr5hqqsp54jk5w/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-http-cookies-6.04-7kzsef2amsex5oidodbr5hqqsp54jk5w/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-http-message-6.13-iviubkzztccupgornclzap7twnewecy5/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-http-message-6.13-iviubkzztccupgornclzap7twnewecy5/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-io-html-1.001-dkhdaunp7yp3xhdqgmoe6axsjfvbk5rl/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-io-html-1.001-dkhdaunp7yp3xhdqgmoe6axsjfvbk5rl/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-lwp-mediatypes-6.02-q4jz653k26lvg2akdxjfmqv7ph5zfyxj/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-lwp-mediatypes-6.02-q4jz653k26lvg2akdxjfmqv7ph5zfyxj/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-try-tiny-0.28-gi2nsz4a6cdmjbxkgth74fta6z67dd5f/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-try-tiny-0.28-gi2nsz4a6cdmjbxkgth74fta6z67dd5f/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-uri-1.72-s5kxucs54nyuz765o5twer57umcd4hso/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-uri-1.72-s5kxucs54nyuz765o5twer57umcd4hso/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-test-needs-0.002005-y6jwhweyon42udslluqa3bkfd4727hd5/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-test-needs-0.002005-y6jwhweyon42udslluqa3bkfd4727hd5/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-http-daemon-6.01-wyh7jnkndum3wdgoeejo5hneowvrscgg/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-http-daemon-6.01-wyh7jnkndum3wdgoeejo5hneowvrscgg/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-module-build-tiny-0.039-fc3dj3r2xi5xfbc46sjl5d76idqo35ms/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-module-build-tiny-0.039-fc3dj3r2xi5xfbc46sjl5d76idqo35ms/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-extutils-config-0.008-mwsyurtfkammachyqf74x7ioua6om5sl/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-extutils-config-0.008-mwsyurtfkammachyqf74x7ioua6om5sl/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-extutils-helpers-0.026-nfibqewdstgvj5nttgfx3goe2drpgvg4/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-extutils-helpers-0.026-nfibqewdstgvj5nttgfx3goe2drpgvg4/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-extutils-installpaths-0.012-uikmhmdulyx2xxycvyaujl5ycw6b2g2b/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-extutils-installpaths-0.012-uikmhmdulyx2xxycvyaujl5ycw6b2g2b/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-module-build-0.4224-wyvmmmx6sls6f3gam2my5ukxfqemxipi/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-module-build-0.4224-wyvmmmx6sls6f3gam2my5ukxfqemxipi/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-http-negotiate-6.01-kpyig5agtyu7zdpor24df3aploypgahn/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-http-negotiate-6.01-kpyig5agtyu7zdpor24df3aploypgahn/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-net-http-6.17-wzv6iryzu2kxbtwuxycvmt7mpfiy5ygr/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-net-http-6.17-wzv6iryzu2kxbtwuxycvmt7mpfiy5ygr/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-www-robotrules-6.02-gucpqzb7agad6mf6l6vn2niuel6mdngx/lib/perl5/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-www-robotrules-6.02-gucpqzb7agad6mf6l6vn2niuel6mdngx/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-5.32.1-3cibemokw65lgp7rvf7wrkelypdl72z5/lib/perl5 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-5.32.1-3cibemokw65lgp7rvf7wrkelypdl72z5/lib/site_perl/5.32.1/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-5.32.1-3cibemokw65lgp7rvf7wrkelypdl72z5/lib/site_perl/5.32.1 /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-5.32.1-3cibemokw65lgp7rvf7wrkelypdl72z5/lib/5.32.1/aarch64-linux-thread-multi /home/spack/spack/opt/spack/linux-centos8-aarch64/gcc-8.3.1/perl-5.32.1-3cibemokw65lgp7rvf7wrkelypdl72z5/lib/5.32.1) at /tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/scripts/meme-chip line 121.

BEGIN failed--compilation aborted at /tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/scripts/meme-chip line 121.

-------------------------------------------------------------------------------

meme-chip exited with value 2 indicating failure.

FAILED!

……

Test tomtom_pearson ...

tomtom -verbosity 1 -dist pearson -oc results/tomtom5 -incomplete-scores common/sample.meme common/sample.meme &> log

reference /tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/tomtom/tomtom.out.pearson.tsv output results/tomtom5/tomtom.tsv

-------------------------------------------------------------------------------

11,13c11,13

< V_CMYB_01 V_CMYB_01 0 1.38238e-28 6.91191e-28 1.38238e-27 18 CCCAACGGCGGTTGGGGG CCCAACGGCGGTTGGGGG +

< V_CMYB_01 V_E47_01 -4 0.0828268 0.414134 0.276089 14 CCCAACGGCGGTTGGGGG ACGGCAGGTGTCCCC +

< V_CMYB_01 V_MYOD_01 -5 0.148933 0.744665 0.372332 12 CCCAACGGCGGTTGGGGG CAACAGGTGGTG +

---

> V_CMYB_01 V_CMYB_01 0 6.24232e-28 3.12116e-27 6.24232e-27 18 CCCAACGGCGGTTGGGGG CCCAACGGCGGTTGGGGG +

> V_CMYB_01 V_E47_01 -4 0.0799662 0.399831 0.266554 14 CCCAACGGCGGTTGGGGG ACGGCAGGTGTCCCC +

> V_CMYB_01 V_MYOD_01 -5 0.146173 0.730864 0.365432 12 CCCAACGGCGGTTGGGGG CAACAGGTGGTG +

reference /tmp/root/spack-stage/spack-stage-meme-5.3.0-qp5yepvlj7xjovlrzgh2al45yxgxparm/spack-src/tests/tomtom/tomtom.out.pearson.html output results/tomtom5/tomtom.html

A difference was detected between the reference and tested json files.

Got data:all_matches@4:matches@1:pv="1.38e-28" but expected data:all_matches@4:matches@1:pv="6.24e-28".

FAILED!

I want to know why there are four cases: fasta-dinucleotide-shuffle1 fimo2 meme-chip1 tomtom_pearson failure. Is it my test dependency incomplete? However, I have added all test dependencies in the sppack according to the instructions. If there is a problem with the original test source code, please let me know.

[root@centos8 spack-src]# spack debug report

* **Spack:** 0.16.1-1935-14c7a13893

* **Python:** 3.6.8

* **Platform:** linux-centos8-aarch64

* **Concretizer:** original

cegrant

unread,

Apr 14, 2021, 8:40:48 PM4/14/21

to MEME Suite Q&A

First I'd note that the latest version of the MEME Suite is 5.3.3. You probably want to install that one instead.

There is a known error with the test for fasta-dinucleotide-shuffle. Python 3 changed the random number generator from Python 2, so you end up getting different shuffles than expected if you are using Python 3. This should be fixed in the next release. In the meantime you can ignore errors in this test.

The failure in meme-chip includes the message:

Test meme-chip1 ...

meme-chip -oc results/meme-chip1 -db meme-chip/JASPAR_CORE_2014_vertebrates.meme meme-chip/Klf1.100.fa &> log

Can't locate XML/Simple.pm in @INC (you may need to install the XML::Simple module)

This means you are missing the Perl module XML::Simple. In the directory 'scripts' you'll find a Perl script named 'dependencies.pl'. If you run 'perl dependencies.pl' it will list the Perl module you are missing.

It also looks like the DREME test completely failed to run. If you look in tests/scripts you should find a file name deme.log which should have more information about the failure.

More curious are the failures with FIMO and tomtom_pearson. It looks like the tomtom_pearson test is generating some floating point results that are very slightly off from what is expected. For example:

V_CMYB_01 V_CMYB_01 0 1.38238e-28

vs the expected result

V_CMYB_01 V_CMYB_01 0 6.24232e-28

The difference is very small, but the test just does a literal character by character comparison, so it fails. Is this very old or very new hardware or OS?

The fimo2 test seems to be failing because some of the FIMO results are on different lines than expected. You'd have to examine the FIMO output in tests/results/fimo2/fimo.tsv and compare them to the expected output in tests/fimo/fimo-motif23.tsv to see what is going on.

Liz Ing-Simmons

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Sep 13, 2023, 8:42:54 AM9/13/23

to MEME Suite Q&A

Hello,

I'm getting these exact same test failures (except the one for meme-chip) with MEME 5.4.1. I was wondering if any progress was made figuring out the cause? Please see details below and please let me know if any additional information would be helpful!

Thanks,
Liz

---

Details:
Mac OS Ventura 13.4.1

Perl v5.30.3

Python 3.11.4 (python 2 is not on my PATH but seems to be used by make check, see below)

Subset of `make check` output:

PASS: dreme2
PASS: fasta-center1

Using python 2

FAIL: fasta-dinucleotide-shuffle1 (differences in stdout)
PASS: fimo1
FAIL: fimo2 (differences in fimo.tsv)

[...]

PASS: tomtom_kullback
FAIL: tomtom_pearson (differences in tomtom.html)
PASS: tomtom_sandelin

[...]

PASS: xstreme5
============================================================================
Testsuite summary for meme 5.4.1
============================================================================
# TOTAL: 174
# PASS: 171

# SKIP: 0
# XFAIL: 0

# FAIL: 3
# XPASS: 0
# ERROR: 0
============================================================================
See tests/scripts/test-suite.log
============================================================================

Relevant parts of tests/scripts/test-suite.log:

RUN: 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_F7gWx_stdout 2> log
reference common/Klf1-200-100-shuffled.py2.fa output results/fasta-dinucleotide-shuffle1/fasta-dinucleotide-shuffle_F7gWx_stdout

-------------------------------------------------------------------------------
2c2
< AGCAAACCATCCACTAATACGCACTGTTGACTCTACTGATAGAATCTGCCTGAACGACCAAAGAACACTTCCAGCAATTCAGCACACCCATGAGACGCCA
---
> AAAGACCCTGACCACACACTGCTTGATGCCGAAGAAGCAAACTTTACCTACATGACTCTCGAATATCCACACCCATCACACTCAGCATAAAGCGAGTGCA
4c4
< AGCCCACCTGAATCAGGAGATACATAGATTGGAATGCTCTGAAGTGTCAAATGTCCCTCTCTGTTCCAGCACTTTTCTCTGAAGTAAGCCTTCCAACCTA

---

[...]

> TCTCCTGTTTCTCCCCTTGTGGCTGGCCTCTACTGAGTAGTCCGGGTCAAGAAGACACTTTAGATGCTTGCCTGGGCCCAGTGAGGGCTGGCTTAGGAAT
338c338
< GATCATTTCAAGCCAAGGCTTCGGAGTGCAGGAACATGAAATGTGCAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
---
> GAATGAAAGAGCAATCTCATTTGGTTGCACATCGTGAAAGGGCCAGCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
FAILED!

[...]

Test fimo2 ...
fimo --oc results/fimo2 --motif CGGYGGGG --motif GCATCRGRBSAGA --no-qvalue --motif-pseudo 0.01 --thresh 0.01 common/crp0.meme.xml /Users/egi12/software/meme-5.4.1/tests/motiph/spiked.fasta &> log

Skipping motif +TKTGANCNABNTCACAHWT.
Skipping motif -TKTGANCNABNTCACAHWT.
Using motif +CGGYGGGG of width 8.
Using motif -CGGYGGGG of width 8.
Using motif +GCATCRGRBSAGA of width 13.
Using motif -GCATCRGRBSAGA of width 13.

reference /Users/egi12/software/meme-5.4.1/tests/fimo/fimo-motif23.tsv output results/fimo2/fimo.tsv
-------------------------------------------------------------------------------
14d13
< CGGYGGGG MEME-2 Scer 2130 2137 + -3.73469 0.00441 0 CTTTGGGG
15a15
> CGGYGGGG MEME-2 Scer 2130 2137 + -3.73469 0.00441 0 CTTTGGGG
20d19
< GCATCRGRBSAGA MEME-3 Scer 1640 1652 - -20.0899 0.00629 0 TATTCAAGCGAGA
21a21
> GCATCRGRBSAGA MEME-3 Scer 1640 1652 - -20.0899 0.00629 0 TATTCAAGCGAGA
25,28d24
< CGGYGGGG MEME-2 Scer 226 233 + -12.2449 0.00808 0 CATAGGGG
< CGGYGGGG MEME-2 Scer 326 333 + -12.2449 0.00808 0 CGGAGCGT
< CGGYGGGG MEME-2 Scer 972 979 + -12.2449 0.00808 0 TGGAGTGG
< CGGYGGGG MEME-2 Scer 1696 1703 + -12.2449 0.00808 0 CTTAGGGG
33a30,33
> CGGYGGGG MEME-2 Scer 226 233 + -12.2449 0.00808 0 CATAGGGG
> CGGYGGGG MEME-2 Scer 326 333 + -12.2449 0.00808 0 CGGAGCGT
> CGGYGGGG MEME-2 Scer 972 979 + -12.2449 0.00808 0 TGGAGTGG
> CGGYGGGG MEME-2 Scer 1696 1703 + -12.2449 0.00808 0 CTTAGGGG
FAILED!

[...]

Test tomtom_pearson ...
tomtom -verbosity 1 -dist pearson -oc results/tomtom5 -incomplete-scores common/sample.meme common/sample.meme &> log

reference /Users/egi12/software/meme-5.4.1/tests/tomtom/tomtom.out.pearson.tsv output results/tomtom5/tomtom.tsv

-------------------------------------------------------------------------------
11,13c11,13
< V_CMYB_01 V_CMYB_01 0 1.38238e-28 6.91191e-28 1.38238e-27 18 CCCAACGGCGGTTGGGGG CCCAACGGCGGTTGGGGG +
< V_CMYB_01 V_E47_01 -4 0.0828268 0.414134 0.276089 14 CCCAACGGCGGTTGGGGG ACGGCAGGTGTCCCC +
< V_CMYB_01 V_MYOD_01 -5 0.148933 0.744665 0.372332 12 CCCAACGGCGGTTGGGGG CAACAGGTGGTG +
---
> V_CMYB_01 V_CMYB_01 0 6.24232e-28 3.12116e-27 6.24232e-27 18 CCCAACGGCGGTTGGGGG CCCAACGGCGGTTGGGGG +
> V_CMYB_01 V_E47_01 -4 0.0799662 0.399831 0.266554 14 CCCAACGGCGGTTGGGGG ACGGCAGGTGTCCCC +
> V_CMYB_01 V_MYOD_01 -5 0.146173 0.730864 0.365432 12 CCCAACGGCGGTTGGGGG CAACAGGTGGTG +

reference /Users/egi12/software/meme-5.4.1/tests/tomtom/tomtom.out.pearson.html output results/tomtom5/tomtom.html

A difference was detected between the reference and tested json files.
Got data:all_matches@4:matches@1:pv="1.38e-28" but expected data:all_matches@4:matches@1:pv="6.24e-28".
FAILED!

cegrant

unread,

Sep 13, 2023, 4:28:40 PM9/13/23

to MEME Suite Q&A

Hi Liz,

The previous user's issue was due changes in the output of the random number generator between Python 2 and Python 3. It's a bit odd that the DREME test thinks you are using Python 2 when it is not on your PATH. However, before we did into why that might be, let me mention a few things. MEME Suite is up to version 5.5.4, so 5.4.1 is a couple of years out of date. Before spending a lot of time debugging this problem you may want to upgraded to the latest version. Also, DREME is now deprecated in favor of STREME, so unless your are stuck using DREME for historical reasons, you can probably ignore errors relating to DREME.

Is your computer running on Apple's M1 processor? We found there were a number of small differences in floating point results between M1 and Intel computers, and these in turn could cause slight differences in the results of the test of the Tomtom Pearson scoring, which is one of the tests on your system that is failing. This was fixed in release 5.5.3.

Most of the errors due seem to be ones we've seen due to Python 2 vs Python 3 issues, so if you want to pursuit we'll need to figure out why the tests think they are using Python 2 when you only have Python 3 in your PATH. It would be helpful if you could forward us a copy of the config.log file that was generated when you configured and installed your system. It would also be helpful to have the output of the following command:

which -a python

This will list all the copies of Python in your PATH.

Liz Ing-Simmons

unread,

Sep 14, 2023, 5:24:38 AM9/14/23

to ceg...@uw.edu, MEME Suite Q&A

Hi,

Whoops, I was using the install instructions from memes and I 100% thought I had updated the version number to the most recent one, but I hadn't. I updated to 5.5.4 now and all the tests pass.

My computer is indeed using the M1 processor. Not sure about the python 2 issue, as which -a python returns only `python not found`. But that message is gone with the new version anyway.

Thanks for your help and sorry for the noise!

Cheers,

Liz

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