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Daria Melikhova
Oct 25, 2019, 7:22:09 AM10/25/19
to MEME Suite Q&A
I tried to install meme-suite 5.1.0, but make test had a lot of failed tests.
OS: Ubuntu 18.04
Here what I got
cd tests/scripts; make check
make[1]: Entering directory '/home/daria/meme-5.1.0/tests/scripts'
make test_driver
make[2]: Entering directory '/home/daria/meme-5.1.0/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 '/home/daria/meme-5.1.0/tests/scripts'
make check-TESTS
make[2]: Entering directory '/home/daria/meme-5.1.0/tests/scripts'
make[3]: Entering directory '/home/daria/meme-5.1.0/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)
PASS: ama1
PASS: ama2
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 (missing centrimo.html)
FAIL: centrimo2 (missing centrimo.html)
FAIL: centrimo3 (missing centrimo.html)
FAIL: centrimo4 (missing centrimo.html)
FAIL: centrimo5 (missing centrimo.html)
FAIL: centrimo6 (missing centrimo.html)
FAIL: centrimo7 (missing centrimo.html)
FAIL: centrimo8 (missing centrimo.html)
FAIL: centrimo9 (missing centrimo.html)
FAIL: tgene1 (missing tgene.html)
FAIL: tgene2 (missing tgene.html)
FAIL: tgene3 (missing tgene.html)
FAIL: tgene4 (missing tgene.html)
SKIP: create-priors1
SKIP: create-priors2
SKIP: dreme1
SKIP: dreme2
SKIP: dreme3
SKIP: dreme4
SKIP: fasta-center1
SKIP: fasta-dinucleotide-shuffle1
PASS: fimo1
PASS: fimo2
PASS: fimo3
PASS: fimo4
FAIL: glam2_1 (CRASH!)
FAIL: glam2scan1 (CRASH!)
FAIL: gomo1 (CRASH!)
FAIL: gomo2 (CRASH!)
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
FAIL: mast19 (missing mast.html)
FAIL: mast20 (missing mast.html)
FAIL: mast21 (missing mast.html)
FAIL: mcast1 (missing mcast.html)
FAIL: mcast2 (missing mcast.html)
SKIP: meme1
SKIP: meme2
SKIP: meme3
SKIP: meme4
SKIP: meme5
SKIP: meme6
SKIP: meme7
SKIP: meme8
SKIP: meme9
SKIP: meme10
SKIP: meme11
SKIP: meme12
SKIP: meme13
SKIP: meme14
SKIP: meme15
SKIP: meme16
SKIP: meme17
SKIP: meme18
SKIP: meme_psp
SKIP: meme-chip1
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!)
SKIP: motiph1
SKIP: motiph2
SKIP: psp-gen1
SKIP: psp-gen2
SKIP: psp-gen3
SKIP: qvalue1
SKIP: qvalue2
FAIL: spamo1 (missing spamo.html)
FAIL: spamo2 (missing spamo.html)
FAIL: spamo3 (missing spamo.html)
FAIL: spamo4 (missing spamo.html)
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 5.1.0
============================================================================
# TOTAL: 152
# PASS: 24
# SKIP: 56
# XFAIL: 0
# FAIL: 72
# XPASS: 0
# ERROR: 0
============================================================================
See tests/scripts/test-suite.log
============================================================================
Makefile:579: recipe for target 'test-suite.log' failed
make[3]: *** [test-suite.log] Error 1
make[3]: Leaving directory '/home/daria/meme-5.1.0/tests/scripts'
Makefile:685: recipe for target 'check-TESTS' failed
make[2]: *** [check-TESTS] Error 2
make[2]: Leaving directory '/home/daria/meme-5.1.0/tests/scripts'
Makefile:751: recipe for target 'check-am' failed
make[1]: *** [check-am] Error 2
make[1]: Leaving directory '/home/daria/meme-5.1.0/tests/scripts'
Makefile:1216: recipe for target 'test' failed
make: *** [test] Error 2
make[1]: Entering directory '/home/daria/meme-5.1.0/tests/scripts'
make test_driver
make[2]: Entering directory '/home/daria/meme-5.1.0/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 '/home/daria/meme-5.1.0/tests/scripts'
make check-TESTS
make[2]: Entering directory '/home/daria/meme-5.1.0/tests/scripts'
make[3]: Entering directory '/home/daria/meme-5.1.0/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)
PASS: ama1
PASS: ama2
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 (missing centrimo.html)
FAIL: centrimo2 (missing centrimo.html)
FAIL: centrimo3 (missing centrimo.html)
FAIL: centrimo4 (missing centrimo.html)
FAIL: centrimo5 (missing centrimo.html)
FAIL: centrimo6 (missing centrimo.html)
FAIL: centrimo7 (missing centrimo.html)
FAIL: centrimo8 (missing centrimo.html)
FAIL: centrimo9 (missing centrimo.html)
FAIL: tgene1 (missing tgene.html)
FAIL: tgene2 (missing tgene.html)
FAIL: tgene3 (missing tgene.html)
FAIL: tgene4 (missing tgene.html)
SKIP: create-priors1
SKIP: create-priors2
SKIP: dreme1
SKIP: dreme2
SKIP: dreme3
SKIP: dreme4
SKIP: fasta-center1
SKIP: fasta-dinucleotide-shuffle1
PASS: fimo1
PASS: fimo2
PASS: fimo3
PASS: fimo4
FAIL: glam2_1 (CRASH!)
FAIL: glam2scan1 (CRASH!)
FAIL: gomo1 (CRASH!)
FAIL: gomo2 (CRASH!)
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
FAIL: mast19 (missing mast.html)
FAIL: mast20 (missing mast.html)
FAIL: mast21 (missing mast.html)
FAIL: mcast1 (missing mcast.html)
FAIL: mcast2 (missing mcast.html)
SKIP: meme1
SKIP: meme2
SKIP: meme3
SKIP: meme4
SKIP: meme5
SKIP: meme6
SKIP: meme7
SKIP: meme8
SKIP: meme9
SKIP: meme10
SKIP: meme11
SKIP: meme12
SKIP: meme13
SKIP: meme14
SKIP: meme15
SKIP: meme16
SKIP: meme17
SKIP: meme18
SKIP: meme_psp
SKIP: meme-chip1
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!)
SKIP: motiph1
SKIP: motiph2
SKIP: psp-gen1
SKIP: psp-gen2
SKIP: psp-gen3
SKIP: qvalue1
SKIP: qvalue2
FAIL: spamo1 (missing spamo.html)
FAIL: spamo2 (missing spamo.html)
FAIL: spamo3 (missing spamo.html)
FAIL: spamo4 (missing spamo.html)
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 5.1.0
============================================================================
# TOTAL: 152
# PASS: 24
# SKIP: 56
# XFAIL: 0
# FAIL: 72
# XPASS: 0
# ERROR: 0
============================================================================
See tests/scripts/test-suite.log
============================================================================
Makefile:579: recipe for target 'test-suite.log' failed
make[3]: *** [test-suite.log] Error 1
make[3]: Leaving directory '/home/daria/meme-5.1.0/tests/scripts'
Makefile:685: recipe for target 'check-TESTS' failed
make[2]: *** [check-TESTS] Error 2
make[2]: Leaving directory '/home/daria/meme-5.1.0/tests/scripts'
Makefile:751: recipe for target 'check-am' failed
make[1]: *** [check-am] Error 2
make[1]: Leaving directory '/home/daria/meme-5.1.0/tests/scripts'
Makefile:1216: recipe for target 'test' failed
make: *** [test] Error 2
And that is my log file
==============================================
meme 5.1.0: tests/scripts/test-suite.log
==============================================
# TOTAL: 152
# PASS: 24
# SKIP: 56
# XFAIL: 0
# FAIL: 72
# XPASS: 0
# ERROR: 0
.. contents:: :depth: 2
RUN: motif-in
=============
*******************************************************************************
Generating meme motifs...
meme -oc results/motif.meme.crp0 -nostatus -p 5 -dna -nmotifs 3 common/crp0.s
sh: 1: /home/daria/meme-5.1.0/src/parallel/meme: not found
*******************************************************************************
Test motif-in.meme.crp0.text ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.crp0.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.crp0.html ...
SKIPPED!
*******************************************************************************
Generating meme motifs...
meme -oc results/motif.meme.lipocalin -nostatus -p 5 -protein -nmotifs 3 common/lipocalin.s
sh: 1: /home/daria/meme-5.1.0/src/parallel/meme: not found
*******************************************************************************
Test motif-in.meme.lipocalin.text ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.lipocalin.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.lipocalin.html ...
SKIPPED!
*******************************************************************************
Generating meme motifs...
meme -oc results/motif.meme.puf3p -nostatus -p 5 -rna -nmotifs 3 common/Puf3p-20.s
sh: 1: /home/daria/meme-5.1.0/src/parallel/meme: not found
*******************************************************************************
Test motif-in.meme.puf3p.text ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.puf3p.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.puf3p.html ...
SKIPPED!
*******************************************************************************
Generating meme motifs...
meme -oc results/motif.meme.crp0.extdna -nostatus -p 5 -alph common/extended_dna.alph -nmotifs 3 common/crp0.s
sh: 1: /home/daria/meme-5.1.0/src/parallel/meme: not found
*******************************************************************************
Test motif-in.meme.crp0.extdna.text ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.crp0.extdna.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.crp0.extdna.html ...
SKIPPED!
*******************************************************************************
Generating dreme motifs...
dreme -oc results/motif.dreme.klf1 -m 2 -p common/Klf1-200-100.fa -n common/Klf1-200-100-shuffled.fa
sh: 1: /home/daria/meme-5.1.0/scripts/dreme: not found
*******************************************************************************
Test motif-in.dreme.klf1.text ...
SKIPPED!
*******************************************************************************
Test motif-in.dreme.klf1.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.dreme.klf1.html ...
SKIPPED!
*******************************************************************************
Generating dreme motifs...
dreme -oc results/motif.dreme.klf1.extdna -alph common/extended_dna.alph -m 2 -p common/Klf1-200-100.fa -n common/Klf1-200-100-shuffled.fa
sh: 1: /home/daria/meme-5.1.0/scripts/dreme: not found
*******************************************************************************
Test motif-in.dreme.klf1.extdna.text ...
SKIPPED!
*******************************************************************************
Test motif-in.dreme.klf1.extdna.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.dreme.klf1.extdna.html ...
SKIPPED!
*******************************************************************************
Generating dreme motifs...
dreme -oc results/motif.dreme.puf3p -rna -m 3 -p common/Puf3p.s
sh: 1: /home/daria/meme-5.1.0/scripts/dreme: not found
*******************************************************************************
Test motif-in.dreme.puf3p.text ...
SKIPPED!
*******************************************************************************
Test motif-in.dreme.puf3p.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.dreme.puf3p.html ...
SKIPPED!
RUN: ama
========
*******************************************************************************
Test ama1 ...
ama --verbosity 1 --scoring max-odds gomo/motif.meme.txt gomo/seqs.fasta gomo/seqs.bg 1> results/ama1/ama_MDF_X_stdout 2> log
reference gomo/ama.withMaxodds.xml output results/ama1/ama_MDF_X_stdout
PASSED!
*******************************************************************************
Test ama2 ...
ama --pvalues --verbosity 1 --cs gomo/motif.meme.txt gomo/seqs_red.fasta gomo/seqs.norc.bg 1> results/ama2/ama_0PZsO_stdout 2> log
reference gomo/ama.redundant.xml output results/ama2/ama_0PZsO_stdout
PASSED!
RUN: ame
========
*******************************************************************************
Test ame1 ...
ame --verbose 1 --method fisher --scoring totalhits --oc results/ame1 --evalue-report-threshold 2 --hit-lo-fraction 0.85 --bgfile --uniform-- common/Klf1-200-100.combined.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame2 ...
ame --verbose 1 --method fisher --scoring totalhits --oc results/ame2 --evalue-report-threshold 2 --hit-lo-fraction 0.85 --bgfile --motif-- -motif-pseudo 0 --control --shuffle-- --seed 5 common/Klf1-200-100.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame3 ...
ame --verbose 1 --method fisher --scoring totalhits --oc results/ame3 --evalue-report-threshold 2 --hit-lo-fraction 0.85 --fix-partition 169 common/Klf1-200-100.combined.nofasta.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame4 ...
ame --verbose 1 --method fisher --scoring avg --oc results/ame4 --evalue-report-threshold 2 --bgfile --uniform-- --poslist fasta --hit-lo-fraction 0.85 common/Klf1-200-100.combined.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame5 ...
ame --verbose 1 --method fisher --scoring avg --oc results/ame5 --evalue-report-threshold 2 --bgfile --motif-- -motif-pseudo 0 --control --shuffle-- --kmer 1 common/Klf1-200-100.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame6 ...
ame --verbose 1 --method fisher --scoring avg --oc results/ame6 --evalue-report-threshold 2 --fix-partition 169 common/Klf1-200-100.combined.nofasta.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame7 ...
ame --verbose 1 --method ranksum --scoring totalhits --oc results/ame7 --evalue-report-threshold 100 --hit-lo-fraction 0.85 --bgfile --uniform-- common/Klf1-200-100.combined.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame8 ...
ame --verbose 1 --method ranksum --scoring totalhits --oc results/ame8 --evalue-report-threshold 100 --hit-lo-fraction 0.85 --bgfile --motif-- -motif-pseudo 0 --control common/Klf1-200-100-shuffled.fa common/Klf1-200-100.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame9 ...
ame --verbose 1 --method ranksum --scoring totalhits --oc results/ame9 --evalue-report-threshold 100 --hit-lo-fraction 0.85 --fix-partition 169 common/Klf1-200-100.combined.nofasta.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame10 ...
ame --verbose 1 --method ranksum --scoring avg --oc results/ame10 --evalue-report-threshold 100 --bgfile --uniform-- --poslist fasta --hit-lo-fraction 0.85 common/Klf1-200-100.combined.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame11 ...
ame --verbose 1 --method ranksum --scoring avg --oc results/ame11 --evalue-report-threshold 100 --bgfile --motif-- -motif-pseudo 0 --control common/Klf1-200-100-shuffled.fa common/Klf1-200-100.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame12 ...
ame --verbose 1 --method ranksum --scoring avg --oc results/ame12 --evalue-report-threshold 100 --fix-partition 169 common/Klf1-200-100.combined.nofasta.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame13 ...
ame --oc results/ame13 --verbose 1 --xalph common/dna_with_covalent.alph --inc MA00\* --inc MA04\* --exc MA007\* --inc T\* --bgfile common/dna_with_covalent.bg --kmer 1 --control --shuffle-- --motif-pseudo 1 common/dna_with_covalent.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme common/dna_with_covalent.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
RUN: centrimo
=============
*******************************************************************************
Test centrimo1 ...
centrimo --verbosity 1 --oc results/centrimo1 --flip --motif-pseudo 1 common/Klf1.fa centrimo/dreme-Klf1.xml &> log
Failed to open html template file
reference centrimo/seq_bg_site_counts.txt output results/centrimo1/site_counts.txt
reference centrimo/seq_bg_centrimo.tsv output results/centrimo1/centrimo.tsv
-------------------------------------------------------------------------------
centrimo did not create the file "results/centrimo1/centrimo.html"
FAILED!
*******************************************************************************
Test centrimo2 ...
centrimo --verbosity 1 --oc results/centrimo2 --flip --bfile --motif-- --motif-pseudo 1 common/Klf1.fa centrimo/dreme-Klf1.xml &> log
Failed to open html template file
reference centrimo/motif_bg_site_counts.txt output results/centrimo2/site_counts.txt
reference centrimo/motif_bg_centrimo.tsv output results/centrimo2/centrimo.tsv
-------------------------------------------------------------------------------
centrimo did not create the file "results/centrimo2/centrimo.html"
FAILED!
*******************************************************************************
Test centrimo3 ...
centrimo --verbosity 1 --oc results/centrimo3 --flip --bfile --uniform-- --motif-pseudo 1 common/Klf1.fa centrimo/dreme-Klf1.xml &> log
Failed to open html template file
reference centrimo/uni_bg_site_counts.txt output results/centrimo3/site_counts.txt
reference centrimo/uni_bg_centrimo.tsv output results/centrimo3/centrimo.tsv
-------------------------------------------------------------------------------
centrimo did not create the file "results/centrimo3/centrimo.html"
FAILED!
*******************************************************************************
Test centrimo4 ...
centrimo --oc results/centrimo4 --verbosity 1 --cd --xalph common/dna_with_covalent.alph --noseq --inc MA00\* --inc MA04\* --exc MA007\* --inc T\* common/dna_with_covalent.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme common/dna_with_covalent.meme &> log
Failed to open html template file
reference centrimo/dna_with_covalent_site_counts.txt output results/centrimo4/site_counts.txt
reference centrimo/dna_with_covalent_centrimo.tsv output results/centrimo4/centrimo.tsv
-------------------------------------------------------------------------------
centrimo did not create the file "results/centrimo4/centrimo.html"
FAILED!
*******************************************************************************
Test centrimo5 ...
centrimo --verbosity 1 --oc results/centrimo5 --neg common/Klf1-200.fa --motif-pseudo 1 common/Klf1.fa common/Jaspar-subset.meme &> log
Failed to open html template file
reference centrimo/neg_site_counts.txt output results/centrimo5/site_counts.txt
reference centrimo/neg_centrimo.tsv output results/centrimo5/centrimo.tsv
-------------------------------------------------------------------------------
centrimo did not create the file "results/centrimo5/centrimo.html"
FAILED!
*******************************************************************************
Test centrimo6 ...
centrimo --verbosity 1 --oc results/centrimo6 --cd -flip --motif-pseudo 1 --ethresh 1e-43 common/Klf1.fa centrimo/dreme-Klf1.xml &> log
Failed to open html template file
reference centrimo/cd_seq_bg_site_counts.txt output results/centrimo6/site_counts.txt
reference centrimo/cd_seq_bg_centrimo.tsv output results/centrimo6/centrimo.tsv
-------------------------------------------------------------------------------
centrimo did not create the file "results/centrimo6/centrimo.html"
FAILED!
*******************************************************************************
Test centrimo7 ...
centrimo --verbosity 1 --oc results/centrimo7 --ethresh 0.03 --local --sep --neg common/Klf1-200.fa --motif-pseudo 1 --bfile common/non-uniform.bg common/Klf1.fa common/Jaspar-subset.meme &> log
Failed to open html template file
reference centrimo/local_neg_site_counts.txt output results/centrimo7/site_counts.txt
reference centrimo/local_neg_centrimo.tsv output results/centrimo7/centrimo.tsv
-------------------------------------------------------------------------------
centrimo did not create the file "results/centrimo7/centrimo.html"
FAILED!
*******************************************************************************
Test centrimo8 ...
centrimo --verbosity 1 --oc results/centrimo8 --neg common/Klf1-200.fa --use-lo-fraction --motif-pseudo 1 common/Klf1.fa common/Jaspar-subset.meme &> log
Failed to open html template file
reference centrimo/neg_lo_site_counts.txt output results/centrimo8/site_counts.txt
reference centrimo/neg_lo_centrimo.tsv output results/centrimo8/centrimo.tsv
-------------------------------------------------------------------------------
centrimo did not create the file "results/centrimo8/centrimo.html"
FAILED!
*******************************************************************************
Test centrimo9 ...
centrimo --verbosity 1 --oc results/centrimo9 --neg common/Klf1-200.fa --use-pvalues --score 0.1 --motif-pseudo 1 common/Klf1.fa common/Jaspar-subset.meme &> log
Failed to open html template file
reference centrimo/neg_pv_site_counts.txt output results/centrimo9/site_counts.txt
reference centrimo/neg_pv_centrimo.tsv output results/centrimo9/centrimo.tsv
-------------------------------------------------------------------------------
9c9
< 1 MA0079.1 SP1 KRGGCDGGGT 8.5e-4 7.7e-5 -9.47 0.0 181.0 491 108 198 0.36864 3.2e-7 245 17 44 1.0e0 0.00 1.0e0 -0.00
---
> 1 MA0079.1 SP1 KRGGCDGGGT 8.5e-4 7.7e-5 -9.47 0.0 181.0 491 108 198 0.36864 3.2e-7 245 17 44 1.0e0 0.00 1.0e0 0.00
centrimo did not create the file "results/centrimo9/centrimo.html"
FAILED!
RUN: tgene
==========
*******************************************************************************
Test tgene1 ...
tgene -oc results/tgene1 tgene/P300.2x.bed tgene/gencode.v7.transcripts.chr21.gtf -max-link-distances 500000,1000 -tissues A549,Ag04450,Bj,Gm12878,H1hesc,Helas3,Hepg2,Huvec,K562,Mcf7,Nhek,Sknshra -histone-root tgene/Histone -histones H3k27ac,H3k4me3 -rna-source Cage -expression-root tgene/Expression -no-closest-locus -desc "Predicted links from P300 binding sites to genes on human chromosome 21" -verbosity 1 &> log
Failed to open html template file
reference tgene/p300_links.tsv output results/tgene1/links.tsv
-------------------------------------------------------------------------------
tgene did not create the file "results/tgene1/tgene.html"
FAILED!
*******************************************************************************
Test tgene2 ...
tgene -oc results/tgene2 tgene/P300.2x.bed tgene/gencode.v7.transcripts.chr21.gtf -max-link-distances 500000,1000 -tissues A549,Ag04450,Bj,Gm12878,H1hesc,Helas3,Hepg2,Hmec,Hsmm,Huvec,K562,Mcf7,Nhek,Nhlf,Sknshra -histone-root tgene/Histone -histones H3k27ac,H3k4me3 -rna-source Cage -expression-root tgene/Expression -no-closest-locus -desc "Predicted links from P300 binding sites to genes on human chromosome 21" -verbosity 1 &> log
Failed to open html template file
reference tgene/p300_links.tsv output results/tgene2/links.tsv
-------------------------------------------------------------------------------
tgene did not create the file "results/tgene2/tgene.html"
FAILED!
*******************************************************************************
Test tgene3 ...
tgene -oc results/tgene3 tgene/Rxra.bed tgene/gencode.v7.transcripts.chr21.gtf -max-link-distances 500000 -tissues A549,Ag04450,Bj,Gm12878,H1hesc,Helas3,Hepg2,Huvec,K562,Mcf7,Nhek,Sknshra -rna-source Cage -histone-root tgene/Histone -histones H3k27ac -rna-source Cage -expression-root tgene/Expression -no-closest-locus -no-closest-tss -desc "Predicted links from Rxra binding sites to genes on human chromosome 21 using H3k27ac only" -verbosity 1 &> log
Failed to open html template file
reference tgene/Rxra_links.tsv output results/tgene3/links.tsv
-------------------------------------------------------------------------------
tgene did not create the file "results/tgene3/tgene.html"
FAILED!
*******************************************************************************
Test tgene4 ...
tgene -oc results/tgene4 tgene/P300.2x.bed tgene/gencode.v7.transcripts.chr21.gtf -max-link-distances 500000 -no-closest-locus -desc "Predicted links from P300 binding sites to genes on human chromosome 21 w/o tissue panel" -verbosity 3 &> log
The output directory 'results/tgene4' already exists.
Its contents will be overwritten.
Reading locus file tgene/P300.2x.bed of putative regulatory elements.
Locus file contains 2676 entries.
Removing duplicate regulatory element locus: chr2:24238393-24238843
Removing duplicate regulatory element locus: chr2:26234842-26235800
Removing duplicate regulatory element locus: chr2:28021919-28022522
Removing duplicate regulatory element locus: chr2:30495973-30496739
Removing duplicate regulatory element locus: chr2:30497388-30498100
Removing duplicate regulatory element locus: chr2:30523453-30524041
Removing duplicate regulatory element locus: chr2:36624947-36625626
Removing duplicate regulatory element locus: chr2:36630749-36631433
Removing duplicate regulatory element locus: chr2:42157922-42158452
Removing duplicate regulatory element locus: chr2:42161576-42162039
Removing duplicate regulatory element locus: chr2:44518282-44519021
Removing duplicate regulatory element locus: chr2:46542394-46542880
Removing duplicate regulatory element locus: chr2:47082241-47082973
Removing duplicate regulatory element locus: chr2:47403669-47404015
Removing duplicate regulatory element locus: chr2:56066257-56066711
Removing duplicate regulatory element locus: chr2:62796997-62797771
Removing duplicate regulatory element locus: chr2:67788483-67789212
Removing duplicate regulatory element locus: chr2:70008432-70009022
Removing duplicate regulatory element locus: chr2:72498879-72499731
Removing duplicate regulatory element locus: chr2:85648412-85648941
Removing duplicate regulatory element locus: chr2:86120898-86121424
Removing duplicate regulatory element locus: chr2:101741305-101741923
Removing duplicate regulatory element locus: chr2:107618754-107619177
Removing duplicate regulatory element locus: chr2:107642130-107642947
Removing duplicate regulatory element locus: chr2:110863416-110864165
Removing duplicate regulatory element locus: chr2:113998401-113998986
Removing duplicate regulatory element locus: chr2:138817689-138818184
Removing duplicate regulatory element locus: chr2:138829744-138830278
Removing duplicate regulatory element locus: chr2:150845919-150846404
Removing duplicate regulatory element locus: chr2:161417979-161418392
Removing duplicate regulatory element locus: chr2:164524016-164524415
Removing duplicate regulatory element locus: chr2:173867800-173868253
Removing duplicate regulatory element locus: chr2:173913553-173914375
Removing duplicate regulatory element locus: chr2:173913553-173914375
Removing duplicate regulatory element locus: chr2:175837020-175837430
Removing duplicate regulatory element locus: chr2:178131050-178131609
Removing duplicate regulatory element locus: chr2:188394738-188395172
Removing duplicate regulatory element locus: chr2:191906420-191907072
Removing duplicate regulatory element locus: chr2:191914596-191915690
Removing duplicate regulatory element locus: chr2:192036269-192036961
Removing duplicate regulatory element locus: chr2:192084034-192084612
Removing duplicate regulatory element locus: chr2:196385234-196385981
Removing duplicate regulatory element locus: chr2:201612764-201613273
Removing duplicate regulatory element locus: chr2:206565205-206565907
Removing duplicate regulatory element locus: chr2:211413613-211414144
Removing duplicate regulatory element locus: chr2:221093351-221093881
Removing duplicate regulatory element locus: chr2:221142110-221142799
Removing duplicate regulatory element locus: chr2:226979756-226980240
Removing duplicate regulatory element locus: chr2:226983143-226984266
Removing duplicate regulatory element locus: chr2:227342723-227343457
Removing duplicate regulatory element locus: chr2:228682786-228683880
Removing duplicate regulatory element locus: chr2:228682786-228683880
Removing duplicate regulatory element locus: chr2:234322151-234322954
Removing duplicate regulatory element locus: chr2:234395504-234396432
Removing duplicate regulatory element locus: chr2:234616587-234617246
Removing duplicate regulatory element locus: chr2:235166835-235167329
Removing duplicate regulatory element locus: chr2:235271524-235272157
Removing duplicate regulatory element locus: chr2:236007458-236007964
Removing duplicate regulatory element locus: chr2:239348080-239348489
Removing duplicate regulatory element locus: chr2:239592945-239594073
Removing duplicate regulatory element locus: chr2:239592945-239594073
Removing duplicate regulatory element locus: chr2:241327024-241327413
Removing duplicate regulatory element locus: chr20:10231398-10232057
Removing duplicate regulatory element locus: chr20:11188384-11189027
Removing duplicate regulatory element locus: chr20:11367729-11368355
Removing duplicate regulatory element locus: chr20:14859629-14860404
Removing duplicate regulatory element locus: chr20:14966617-14967287
Removing duplicate regulatory element locus: chr20:22384503-22385026
Removing duplicate regulatory element locus: chr20:22451133-22451545
Removing duplicate regulatory element locus: chr20:30196049-30196807
Removing duplicate regulatory element locus: chr20:30300411-30300945
Removing duplicate regulatory element locus: chr20:36007148-36007949
Removing duplicate regulatory element locus: chr20:36008692-36009296
Removing duplicate regulatory element locus: chr20:36738281-36738821
Removing duplicate regulatory element locus: chr20:43023107-43023572
Removing duplicate regulatory element locus: chr20:43321557-43322071
Removing duplicate regulatory element locus: chr20:45988851-45989313
Removing duplicate regulatory element locus: chr20:46081864-46082401
Removing duplicate regulatory element locus: chr20:48384723-48385508
Removing duplicate regulatory element locus: chr20:48909048-48909559
Removing duplicate regulatory element locus: chr20:48925055-48925685
Removing duplicate regulatory element locus: chr20:50527130-50527698
Removing duplicate regulatory element locus: chr20:52390198-52390995
Removing duplicate regulatory element locus: chr20:52724015-52724768
Removing duplicate regulatory element locus: chr20:52757372-52758023
Removing duplicate regulatory element locus: chr20:52765423-52766015
Removing duplicate regulatory element locus: chr20:55358835-55359349
Removing duplicate regulatory element locus: chr20:56273258-56273802
Removing duplicate regulatory element locus: chr20:56323549-56324068
Removing duplicate regulatory element locus: chr20:56592236-56593268
Removing duplicate regulatory element locus: chr20:56592236-56593268
Removing duplicate regulatory element locus: chr20:61863466-61864363
Removing duplicate regulatory element locus: chr21:16816380-16817396
Removing duplicate regulatory element locus: chr21:16816380-16817396
Removing duplicate regulatory element locus: chr21:38255995-38256567
Removing duplicate regulatory element locus: chr21:39511717-39512242
Removing duplicate regulatory element locus: chr21:39649445-39650105
Removing duplicate regulatory element locus: chr21:44753165-44753648
Removing duplicate regulatory element locus: chr21:44860419-44861441
Removing duplicate regulatory element locus: chr21:44936643-44937264
Removing duplicate regulatory element locus: chr21:45132033-45132841
Removing duplicate regulatory element locus: chr22:30591744-30593090
Removing duplicate regulatory element locus: chr22:30601360-30602148
Removing duplicate regulatory element locus: chr22:30602889-30603428
Removing duplicate regulatory element locus: chr22:30608414-30608975
Removing duplicate regulatory element locus: chr22:35985167-35985852
Removing duplicate regulatory element locus: chr22:40894380-40894991
Removing duplicate regulatory element locus: chr22:40905605-40906153
Removing duplicate regulatory element locus: chr22:45999977-46000616
Removing duplicate regulatory element locus: chr22:46034673-46035548
Removing duplicate regulatory element locus: chr22:46173094-46173754
Removing duplicate regulatory element locus: chr22:48765760-48766512
Locus table contains 2564 valid entries (0 duplicates removed).
Reading the annotation file 'tgene/gencode.v7.transcripts.chr21.gtf'.
The annotation file contained 2183 entries.
Creating the transcript table with 2183 entries.
Removing transcripts for invalid transcript types from the table.
Transcript table now contains 1600 transcripts (583 removed).
Creating the link table based on distance alone.
Distance: 500000
Finding the closest loci to each TSS and creating links.
Finding the closest TSS(es) to each locus.
Created 8772 links.
Computing p-values and q-values for 8772 links
Estimated 8772 Distance p-values.
Converting Distance p-values to q-values.
Estimating pi_0 from all 8772 observed p-values.
Estimating pi_0.
Minimal pi_zero = 0.997405
Estimated pi_0=0.997922
Failed to open html template file
Program ends correctly.
reference tgene/p300_no_panel_links.tsv output results/tgene4/links.tsv
-------------------------------------------------------------------------------
tgene did not create the file "results/tgene4/tgene.html"
FAILED!
RUN: create_priors
==================
*******************************************************************************
Test create-priors1 ...
create-priors -oc results/create-priors1 create-priors/chrX.fa create-priors/DNaseHS_gm12878.wig &> log
Program create-priors not found!
SKIPPED!
*******************************************************************************
Test create-priors2 ...
create-priors -oc results/create-priors2 create-priors/chrX.fa create-priors/DNaseHS_gm12878.wig &> log
Program create-priors not found!
SKIPPED!
RUN: dreme
==========
*******************************************************************************
Test dreme1 ...
dreme -oc results/dreme1 -verbosity 1 -p common/Klf1-200-100.fa -n common/Klf1-200-100-shuffled.fa &> log
Program dreme not found!
SKIPPED!
*******************************************************************************
Test dreme2 ...
dreme -norc -oc results/dreme2 -verbosity 1 -p common/Klf1-200-100.fa -n common/Klf1-200-100-shuffled.fa &> log
Program dreme not found!
SKIPPED!
*******************************************************************************
Test dreme3 ...
dreme-py3 -oc results/dreme3 -verbosity 1 -p common/Klf1-200-100.fa -n common/Klf1-200-100-shuffled.fa &> log
Program dreme-py3 not found!
SKIPPED!
*******************************************************************************
Test dreme4 ...
dreme-py3 -norc -oc results/dreme4 -verbosity 1 -p common/Klf1-200-100.fa -n common/Klf1-200-100-shuffled.fa &> log
Program dreme-py3 not found!
SKIPPED!
RUN: fasta-center
=================
*******************************************************************************
Test fasta-center1 ...
fasta-center -len 100 -dna < common/Klf1-200.fa 1> results/fasta-center1/fasta-center_wJ6aI_stdout 2> log
Program fasta-center not found!
SKIPPED!
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_N_ozB_stdout 2> log
Program fasta-dinucleotide-shuffle not found!
SKIPPED!
RUN: fimo
=========
*******************************************************************************
Test fimo1 ...
fimo --oc results/fimo1 --motif-pseudo 0.01 fimo/MCM1.meme.html fimo/spiked.fasta &> log
Using motif +TTTCCYDWTTBGGAAATW of width 18.
Using motif -TTTCCYDWTTBGGAAATW of width 18.
Computing q-values.
Estimating pi_0 from a uniformly sampled set of 5298 p-values.
Estimating pi_0.
Estimated pi_0=0.799106
reference fimo/fimo.tsv output results/fimo1/fimo.tsv
PASSED!
*******************************************************************************
Test fimo2 ...
fimo --oc results/fimo2 --motif CGGYGGGG --motif GCATCRGRBSAGA --no-qvalue --thresh 0.01 common/crp0.meme.xml 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 fimo/fimo-motif23.tsv output results/fimo2/fimo.tsv
PASSED!
*******************************************************************************
Test fimo3 ...
fimo --oc results/fimo3 --psp fimo/GCN4_YPD.psp --prior-dist fimo/prior.dist.txt fimo/GCN4.meme.txt fimo/GCN4_YPD.fasta &> log
Using motif +MA0303.1 of width 21.
Using motif -MA0303.1 of width 21.
Computing q-values.
Estimating pi_0 from a uniformly sampled set of 10000 p-values.
Estimating pi_0.
Estimated pi_0=1
reference fimo/fimo-priors.tsv output results/fimo3/fimo.tsv
PASSED!
*******************************************************************************
Test fimo4 ...
fimo --oc results/fimo4 --parse-genomic-coord --psp fimo/GCN4_YPD-genomic.psp --prior-dist fimo/prior.dist.txt fimo/GCN4.meme.txt fimo/GCN4_YPD-genomic.fasta &> log
Using motif +MA0303.1 of width 21.
Using motif -MA0303.1 of width 21.
Computing q-values.
Estimating pi_0 from a uniformly sampled set of 10000 p-values.
Estimating pi_0.
Estimated pi_0=1
reference fimo/fimo-priors-genomic.tsv output results/fimo4/fimo.tsv
PASSED!
RUN: glam2
==========
*******************************************************************************
Test glam2_1 ...
glam2 -M -r 3 -n 100 -O results/glam2_1 p common/At.s &> log
The output directory 'results/glam2_1' already exists.
Its contents will be overwritten.
Run 1... 406 iterations
Run 2... 445 iterations
Run 3... 400 iterations
Warning: could not find glam2html script! Failed to convert output to HTML!
Warning: could not find glam2psfm script! Failed to convert to MEME format motif!
-------------------------------------------------------------------------------
glam2 exited with value 1 indicating failure.
FAILED!
RUN: glam2scan
==============
*******************************************************************************
Test glam2scan1 ...
glam2scan -O results/glam2scan1 p glam2/glam2.txt common/At.s &> log
The output directory 'results/glam2scan1' already exists.
Its contents will be overwritten.
Warning: could not find glam2scan2html script! Failed to convert output to HTML!
-------------------------------------------------------------------------------
glam2scan exited with value 1 indicating failure.
FAILED!
RUN: gomo
=========
*******************************************************************************
Test gomo1 ...
gomo --seed 1 --nostatus --verbosity 1 --oc results/gomo1 --motifs gomo/motif.meme.txt gomo/GO2Gene.map.csv gomo/ama.nozscoring.xml &> log
-------------------------------------------------------------------------------
gomo exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test gomo2 ...
gomo --gs --seed 1 --nostatus --verbosity 1 --oc results/gomo2 --motifs gomo/motif.meme.txt gomo/GO2Gene.map.csv gomo/ama.zscoring.xml gomo/ama.nozscoring.xml &> log
-------------------------------------------------------------------------------
gomo exited with value 1 indicating failure.
FAILED!
RUN: mast
=========
*******************************************************************************
Test mast1 ...
mast meme/meme.crp0.classic.oops.txt common/crp0.s -oc results/mast1 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.crp0.classic.oops.txt.xml output results/mast1/mast.xml
PASSED!
*******************************************************************************
Test mast2 ...
mast meme/meme.crp0.classic.zoops.xml common/crp0.s -oc results/mast2 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.crp0.classic.zoops.xml.xml output results/mast2/mast.xml
PASSED!
*******************************************************************************
Test mast3 ...
mast meme/meme.crp0.classic.anr.html common/crp0.s -oc results/mast3 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.crp0.classic.anr.html.xml output results/mast3/mast.xml
PASSED!
*******************************************************************************
Test mast4 ...
mast meme/meme.INO_up800.classic.oops.txt common/INO_up800.s -oc results/mast4 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.INO_up800.classic.oops.txt.xml output results/mast4/mast.xml
PASSED!
*******************************************************************************
Test mast5 ...
mast meme/meme.INO_up800.classic.zoops.xml common/INO_up800.s -oc results/mast5 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.INO_up800.classic.zoops.xml.xml output results/mast5/mast.xml
PASSED!
*******************************************************************************
Test mast6 ...
mast meme/meme.INO_up800.classic.anr.html common/INO_up800.s -oc results/mast6 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.INO_up800.classic.anr.html.xml output results/mast6/mast.xml
PASSED!
*******************************************************************************
Test mast7 ...
mast meme/meme.farntrans5.classic.oops.txt common/farntrans5.s -oc results/mast7 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.farntrans5.classic.oops.txt.xml output results/mast7/mast.xml
PASSED!
*******************************************************************************
Test mast8 ...
mast meme/meme.farntrans5.classic.zoops.xml common/farntrans5.s -oc results/mast8 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.farntrans5.classic.zoops.xml.xml output results/mast8/mast.xml
PASSED!
*******************************************************************************
Test mast9 ...
mast meme/meme.farntrans5.classic.anr.html common/farntrans5.s -oc results/mast9 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.farntrans5.classic.anr.html.xml output results/mast9/mast.xml
PASSED!
*******************************************************************************
Test mast10 ...
mast meme/meme.lipocalin.classic.oops.txt common/lipocalin.s -oc results/mast10 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.lipocalin.classic.oops.txt.xml output results/mast10/mast.xml
PASSED!
*******************************************************************************
Test mast11 ...
mast meme/meme.lipocalin.classic.zoops.xml common/lipocalin.s -oc results/mast11 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.lipocalin.classic.zoops.xml.xml output results/mast11/mast.xml
PASSED!
*******************************************************************************
Test mast12 ...
mast meme/meme.lipocalin.classic.anr.html common/lipocalin.s -oc results/mast12 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.lipocalin.classic.anr.html.xml output results/mast12/mast.xml
PASSED!
*******************************************************************************
Test mast13 ...
mast meme/meme.adh.classic.oops.txt common/adh.s -oc results/mast13 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.adh.classic.oops.txt.xml output results/mast13/mast.xml
PASSED!
*******************************************************************************
Test mast14 ...
mast meme/meme.adh.classic.oops.txt - -oc results/mast14 -nostatus -df stdin -dna -seqp < common/mini-drosoph.s &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.adh.classic.oops.mini-drosoph.txt.xml output results/mast14/mast.xml
PASSED!
*******************************************************************************
Test mast15 ...
mast meme/meme.adh.classic.zoops.html common/adh.s -oc results/mast15 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.adh.classic.zoops.html.xml output results/mast15/mast.xml
PASSED!
*******************************************************************************
Test mast16 ...
mast meme/meme.adh.classic.zoops.html - -oc results/mast16 -nostatus -df stdin -dna -seqp < common/mini-drosoph.s &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.adh.classic.zoops.mini-drosoph.html.xml output results/mast16/mast.xml
PASSED!
*******************************************************************************
Test mast17 ...
mast meme/meme.adh.classic.anr.xml common/adh.s -oc results/mast17 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.adh.classic.anr.xml.xml output results/mast17/mast.xml
PASSED!
*******************************************************************************
Test mast18 ...
mast meme/meme.adh.classic.anr.xml - -oc results/mast18 -nostatus -df stdin -dna -seqp < common/mini-drosoph.s &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.adh.classic.anr.mini-drosoph.xml.xml output results/mast18/mast.xml
PASSED!
*******************************************************************************
Test mast19 ...
mast meme/meme.INO_up800.classic.anr.txt common/INO_up800.s -oc results/mast19 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
-------------------------------------------------------------------------------
mast did not create the file "results/mast19/mast.html"
FAILED!
*******************************************************************************
Test mast20 ...
mast meme/meme.INO_up800.classic.anr.xml common/INO_up800.s -oc results/mast20 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
-------------------------------------------------------------------------------
mast did not create the file "results/mast20/mast.html"
FAILED!
*******************************************************************************
Test mast21 ...
mast meme/meme.INO_up800.classic.anr.html common/INO_up800.s -oc results/mast21 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
-------------------------------------------------------------------------------
mast did not create the file "results/mast21/mast.html"
FAILED!
RUN: mcast
==========
*******************************************************************************
Test mcast1 ...
mcast -oc results/mcast1 meme/meme.lex0.zoops.txt common/lex0.s &> log
Creating HMM from motif array.
Building HMM: (0) 1 2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21 | 22-23-24-25-26-27-28-29-30-31-32-33-34-35-36-37-38-39-40-41 | (42)
Reading sequences in blocks of 232558 characters.
Warning: Cannot estimate pi_0 accurately from fewer than 100 p-values. total p-values = 14. Using pi_zero = 1.0.
User time for computation: 0.002363 seconds
System time for computation: 0 seconds
Failed to open html template file /home/daria/meme-5.1.0/etc/mcast_template.html.
User time for output: 0.000125 seconds
System time for output: 0 seconds
Total user time: 0.002488 seconds
Total system time: 0 seconds
reference mcast/lex0.zoops.tsv output results/mcast1/mcast.tsv
reference mcast/lex0.zoops.gff output results/mcast1/mcast.gff
reference mcast/lex0.zoops.xml output results/mcast1/mcast.xml
reference mcast/lex0.zoops.cisml output results/mcast1/cisml.xml
-------------------------------------------------------------------------------
mcast did not create the file "results/mcast1/mcast.html"
FAILED!
*******************************************************************************
Test mcast2 ...
mcast -oc results/mcast2 -parse-genomic-coord fimo/GCN4.meme.txt fimo/GCN4_YPD-genomic.fasta &> log
Creating HMM from motif array.
Building HMM: (0) 1 2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22 | 23-24-25-26-27-28-29-30-31-32-33-34-35-36-37-38-39-40-41-42-43 | (44)
Reading sequences in blocks of 222222 characters.
Warning: Cannot estimate pi_0 accurately from fewer than 100 p-values. total p-values = 34. Using pi_zero = 1.0.
User time for computation: 0.007069 seconds
System time for computation: 0 seconds
Failed to open html template file /home/daria/meme-5.1.0/etc/mcast_template.html.
User time for output: 0.000114 seconds
System time for output: 0 seconds
Total user time: 0.007183 seconds
Total system time: 0 seconds
reference mcast/parse_genomic.tsv output results/mcast2/mcast.tsv
reference mcast/parse_genomic.gff output results/mcast2/mcast.gff
reference mcast/parse_genomic.xml output results/mcast2/mcast.xml
reference mcast/parse_genomic.cisml output results/mcast2/cisml.xml
-------------------------------------------------------------------------------
mcast did not create the file "results/mcast2/mcast.html"
FAILED!
RUN: meme
=========
*******************************************************************************
Test meme1 ...
meme -p 5 common/crp0.s -oc results/meme1 -mod oops -dna -revcomp -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme2 ...
meme -p 5 -minsites 3 -maxsites 17 common/crp0.s -oc results/meme2 -mod zoops -dna -revcomp -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme3 ...
meme -p 5 -minsites 3 -maxsites 17 common/crp0.s -oc results/meme3 -mod anr -dna -revcomp -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme4 ...
meme -p 5 common/adh.s -oc results/meme4 -mod oops -protein -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme5 ...
meme -p 5 -nsites 27 common/adh.s -oc results/meme5 -mod zoops -protein -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme6 ...
meme -p 5 -nsites 27 common/adh.s -oc results/meme6 -mod anr -protein -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme7 ...
meme -p 5 -csites 30 common/Klf1-200-100.fa -oc results/meme7 -mod oops -dna -revcomp -brief 0 -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme8 ...
meme -p 5 -csites 30 common/Klf1-200-100.fa -oc results/meme8 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme9 ...
meme -p 5 -csites 30 common/Klf1-200-100.fa -oc results/meme9 -mod anr -dna -revcomp -brief 0 -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme10 ...
meme -p 5 common/crp0.s -oc results/meme10 -mod oops -dna -revcomp -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme11 ...
meme -p 5 -minsites 3 -maxsites 17 common/crp0.s -oc results/meme11 -mod zoops -dna -revcomp -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme12 ...
meme -p 5 -minsites 3 -maxsites 17 common/crp0.s -oc results/meme12 -mod anr -dna -revcomp -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme13 ...
meme -p 5 common/adh.s -oc results/meme13 -mod oops -protein -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme14 ...
meme -p 5 -nsites 27 common/adh.s -oc results/meme14 -mod zoops -protein -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme15 ...
meme -p 5 -nsites 27 common/adh.s -oc results/meme15 -mod anr -protein -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme16 ...
meme -p 5 common/Klf1-200-100.fa -oc results/meme16 -mod oops -dna -revcomp -brief 0 -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme17 ...
meme -p 5 common/Klf1-200-100.fa -oc results/meme17 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme18 ...
meme -p 5 common/Klf1-200-100.fa -oc results/meme18 -mod anr -dna -revcomp -brief 0 -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme_psp ...
meme -p 5 common/psp_test.s -oc results/meme19 -psp common/psp_test.psp -minsites 5 -dna -revcomp -minw 7 -maxw 12 -nostatus -searchsize 0 &> log
Program meme not found!
SKIPPED!
RUN: meme-chip
==============
*******************************************************************************
Test meme-chip1 ...
meme-chip -oc results/meme-chip1 -db meme-chip/JASPAR_CORE_2014_vertebrates.meme meme-chip/Klf1.100.fa &> log
Program meme-chip not found!
SKIPPED!
RUN: momo
=========
*******************************************************************************
Test momo1 ...
momo simple --oc results/momo1 --sequence-column sequence momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo2 ...
momo simple --oc results/momo2 --psm-type tide --protein-database momo/small-yeast.fasta --width 11 momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo3 ...
momo simple --oc results/momo3 --psm-type tide --single-motif-per-mass momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo4 ...
momo simple --oc results/momo4 --psm-type tide --protein-database momo/small-yeast.fasta --width 11 --hash-fasta 0 momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo5 ...
momo simple --oc results/momo5 --psm-type tide --eliminate-repeats 3 --protein-database momo/small-yeast.fasta momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo6 ...
momo simple --oc results/momo6 --psm-type tide --eliminate-repeats 0 momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo7 ...
momo simple --oc results/momo7 --psm-type tide --filter "xcorr rank,le,3" momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo8 ...
momo simple --oc results/momo8 --protein-database momo/small-yeast.fasta momo/small-tide-mod-phospho.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo9 ...
momo simple --oc results/momo9 --protein-database momo/small-yeast.fasta momo/small-tide-mod-phospho.fasta &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo10 ...
momo simple --oc results/momo10 --psm-type tide momo/small-tide-mod-1-out-of-2.txt momo/small-tide-mod-2-out-of-2.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo11 ...
momo motifx --oc results/momo11 --psm-type tide --protein-database momo/small-yeast.fasta --score-threshold 0.05 --min-occurrences 1 --harvard --seed 273 momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo12 ...
momo motifx --oc results/momo12 --psm-type tide --db-background --protein-database momo/small-yeast.fasta --score-threshold 0.05 --min-occurrences 1 --single-motif-per-mass --harvard momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo13 ...
momo motifx --oc results/momo13 --db-background --protein-database momo/small-yeast.fasta --score-threshold 0.05 --min-occurrences 1 momo/small-tide-mod-phospho.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo14 ...
momo motifx --oc results/momo14 --db-background --protein-database momo/small-yeast-prealigned-no-unknowns.txt --score-threshold 0.05 --min-occurrences 1 momo/small-tide-mod-phospho.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo15 ...
momo simple --oc results/momo15 --psm-type ms-gf+ --sequence-column Peptide momo/small-msgf-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo16 ...
momo simple --oc results/momo16 --psm-type comet --sequence-column "modified sequence" momo/small-comet-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo17 ...
momo modl --oc results/momo17 --psm-type tide --protein-database momo/small-yeast.fasta momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo18 ...
momo modl --oc results/momo18 --psm-type tide --db-background --remove-unknowns T --protein-database momo/small-yeast.fasta momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
RUN: motiph
===========
*******************************************************************************
Test motiph1 ...
motiph --seed 0 --bg 2 --pseudocount 0.01 --oc results/motiph1 motiph/spiked.aln motiph/yeast.tree motiph/MCM1.meme.html &> log
Program motiph not found!
SKIPPED!
*******************************************************************************
Test motiph2 ...
motiph --seed 0 --bg 2 --pseudocount 0.01 --oc results/motiph2 --output-pthresh 1 --motif CGGYGGGG --motif GCATCRGRBSAGA motiph/spiked.aln motiph/yeast.tree common/crp0.meme.html &> log
Program motiph not found!
SKIPPED!
RUN: pspgen
===========
*******************************************************************************
Test psp-gen1 ...
psp-gen -revcomp -pos psp-gen/one-peak-dna.fasta -neg psp-gen/all-A.fasta 1> results/pspgen1/psp-gen_P3QNY_stdout 2> log
Program psp-gen not found!
SKIPPED!
*******************************************************************************
Test psp-gen2 ...
psp-gen -protein -maxrange -triples -pos psp-gen/one-peak-protein.fasta -neg psp-gen/all-A.fasta 1> results/pspgen2/psp-gen_BNtXQ_stdout 2> log
Program psp-gen not found!
SKIPPED!
*******************************************************************************
Test psp-gen3 ...
psp-gen -alph common/extended_dna.alph -revcomp -pos psp-gen/one-peak-dna.fasta -neg psp-gen/all-A.fasta 1> results/pspgen1/psp-gen_wquC8_stdout 2> log
Program psp-gen not found!
SKIPPED!
RUN: qvalue
===========
*******************************************************************************
Test qvalue1 ...
qvalue --header 1 --append --column 2 --seed 7718 qvalue/uniform.txt 1> results/qvalue1/qvalue_rkZ8l_stdout 2> log
Program qvalue not found!
SKIPPED!
*******************************************************************************
Test qvalue2 ...
qvalue --null qvalue/null.txt qvalue/observed.txt 1> results/qvalue2/qvalue_4LP0s_stdout 2> log
Program qvalue not found!
SKIPPED!
RUN: spamo
==========
*******************************************************************************
Test spamo1 ...
spamo -oc results/spamo1 -verbosity 1 -margin 20 -shared 1 -bgfile --uniform-- spamo/limits.fasta spamo/primary.meme spamo/secondary.meme &> log
Failed to open html template file.
-------------------------------------------------------------------------------
spamo did not create the file "results/spamo1/spamo.html"
reference spamo/limits.tsv output results/spamo1/spamo.tsv
FAILED!
*******************************************************************************
Test spamo2 ...
spamo -oc results/spamo2 -verbosity 1 -margin 20 -shared 1 -bgfile --motif-- spamo/random.fasta spamo/primary.meme spamo/secondary.meme &> log
Failed to open html template file.
-------------------------------------------------------------------------------
spamo did not create the file "results/spamo2/spamo.html"
reference spamo/random.tsv output results/spamo2/spamo.tsv
FAILED!
*******************************************************************************
Test spamo3 ...
spamo -oc results/spamo3 -verbosity 3 -xalph -primary TGCm1C -keepprimary -margin 20 -shared 1 -inc MA00\* -inc T\* -exc MA007\* common/dna_with_covalent.fa common/dna_with_covalent.meme common/Jaspar-subset.meme common/dna_with_covalent.meme common/dna_with_covalent.meme &> log
The output directory 'results/spamo3' already exists.
Its contents will be overwritten.
Loading Primary Motif (name=TGCm1C)
Loading All Sequences
Loaded 2499 Sequences
Determining Best Primary Matches
Eliminating Sequences Without Primary Matches
Eliminated 1553 Sequences Without Primary Match
Trimming Sequences
Freeing Unneeded Sequences
Loading Secondary Motifs from file 'common/Jaspar-subset.meme'
Discarding motif 'MA0140.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.
Discarding motif 'MA0079.1' in 'common/Jaspar-subset.meme' it matched an -exc pattern.
Discarding motif 'MA0079.2' in 'common/Jaspar-subset.meme' it matched an -exc pattern.
Discarding motif 'MA0163.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.
Discarding motif 'MA0270.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.
Discarding motif 'MA0300.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.
Discarding motif 'MA0309.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.
Discarding motif 'MA0443.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.
Loading Secondary Motifs from file 'common/dna_with_covalent.meme'
Discarding motif 'CCTTCC' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'GCAGCA' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'GCAm1C' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'GCAm7C' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'GCm1C1' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'Gm1TGC' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'Gm7GCA' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'TGCmGC' in file 'common/dna_with_covalent.meme' (non-unique ID).
Warning: The following secondary motifs in 'common/dna_with_covalent.meme' were excluded as they didn't fit in the margin:
Tm1m1m1m1m1m1m1m1m1m1m1m1
Loading Secondary Motifs from file 'common/dna_with_covalent.meme'
Discarding motif 'CCTTCC' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'GCAGCA' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'GCAm1C' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'GCAm7C' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'GCm1C1' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'Gm1TGC' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'Gm7GCA' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'TGCmGC' in file 'common/dna_with_covalent.meme' (non-unique ID).
Warning: The following duplicate secondary motifs in 'common/dna_with_covalent.meme' were excluded:
TGCmGC TGCm1C
Warning: The following secondary motifs in 'common/dna_with_covalent.meme' were excluded as they didn't fit in the margin:
Tm1m1m1m1m1m1m1m1m1m1m1m1
Scanning For Secondary Matches
Scanned 20%
Scanned 40%
Scanned 60%
Scanned 80%
Scanned 100%
Sorting Significant Secondary Motifs
Grouping Redundant Secondary Motifs
Outputting TSV
Failed to open html template file.
run_time cpu= 0.08 real= 0.00
-------------------------------------------------------------------------------
spamo did not create the file "results/spamo3/spamo.html"
reference spamo/dna_with_covalent.tsv output results/spamo3/spamo.tsv
FAILED!
*******************************************************************************
Test spamo4 ...
spamo -oc results/spamo4 -verbosity 1 -margin 20 -shared 1 -bgfile --uniform-- -dumpseqs -primary MA0039.2 -keepprimary -inc MA0039.2 -inc MA0140.1 common/Klf1.fa common/Jaspar-subset.meme common/Jaspar-subset.meme &> log
Failed to open html template file.
-------------------------------------------------------------------------------
spamo did not create the file "results/spamo4/spamo.html"
reference spamo/dumpseqs.tsv output results/spamo4/spamo.tsv
reference spamo/dumpseqs.seqs_MA0039.2_db1_MA0039.2.tsv output results/spamo4/seqs_MA0039.2_db1_MA0039.2.tsv
reference spamo/dumpseqs.seqs_MA0039.2_db1_MA0140.1.tsv output results/spamo4/seqs_MA0039.2_db1_MA0140.1.tsv
FAILED!
RUN: tomtom
===========
*******************************************************************************
Test tomtom1 ...
tomtom -oc results/tomtom1 -verbosity 1 -evalue -thresh 10 -m TGCm1C -mi 3 -xalph -bfile common/dna_with_covalent.bg -dist allr common/dna_with_covalent.meme common/dna_with_covalent.meme common/Jaspar-subset.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_allr ...
tomtom -verbosity 1 -dist allr -oc results/tomtom2 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_ed ...
tomtom -verbosity 1 -dist ed -oc results/tomtom3 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_kullback ...
tomtom -verbosity 1 -dist kullback -oc results/tomtom4 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_pearson ...
tomtom -verbosity 1 -dist pearson -oc results/tomtom5 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_sandelin ...
tomtom -verbosity 1 -dist sandelin -oc results/tomtom6 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_blic1 ...
tomtom -verbosity 1 -dist blic1 -oc results/tomtom7 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_blic5 ...
tomtom -verbosity 1 -dist blic5 -oc results/tomtom8 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_allr_cs ...
tomtom -verbosity 1 -dist allr -oc results/tomtom9 common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_ed_cs ...
tomtom -verbosity 1 -dist ed -oc results/tomtom10 common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_kullback_cs ...
tomtom -verbosity 1 -dist kullback -oc results/tomtom11 common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_pearson_cs ...
tomtom -verbosity 1 -dist pearson -oc results/tomtom12 common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_sandelin_cs ...
tomtom -verbosity 1 -dist sandelin -oc results/tomtom13 common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_blic1_cs ...
tomtom -verbosity 1 -dist blic1 -oc results/tomtom14 common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_blic5_cs ...
tomtom -verbosity 1 -dist blic5 -oc results/tomtom15 common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
meme 5.1.0: tests/scripts/test-suite.log
==============================================
# TOTAL: 152
# PASS: 24
# SKIP: 56
# XFAIL: 0
# FAIL: 72
# XPASS: 0
# ERROR: 0
.. contents:: :depth: 2
RUN: motif-in
=============
*******************************************************************************
Generating meme motifs...
meme -oc results/motif.meme.crp0 -nostatus -p 5 -dna -nmotifs 3 common/crp0.s
sh: 1: /home/daria/meme-5.1.0/src/parallel/meme: not found
*******************************************************************************
Test motif-in.meme.crp0.text ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.crp0.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.crp0.html ...
SKIPPED!
*******************************************************************************
Generating meme motifs...
meme -oc results/motif.meme.lipocalin -nostatus -p 5 -protein -nmotifs 3 common/lipocalin.s
sh: 1: /home/daria/meme-5.1.0/src/parallel/meme: not found
*******************************************************************************
Test motif-in.meme.lipocalin.text ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.lipocalin.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.lipocalin.html ...
SKIPPED!
*******************************************************************************
Generating meme motifs...
meme -oc results/motif.meme.puf3p -nostatus -p 5 -rna -nmotifs 3 common/Puf3p-20.s
sh: 1: /home/daria/meme-5.1.0/src/parallel/meme: not found
*******************************************************************************
Test motif-in.meme.puf3p.text ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.puf3p.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.puf3p.html ...
SKIPPED!
*******************************************************************************
Generating meme motifs...
meme -oc results/motif.meme.crp0.extdna -nostatus -p 5 -alph common/extended_dna.alph -nmotifs 3 common/crp0.s
sh: 1: /home/daria/meme-5.1.0/src/parallel/meme: not found
*******************************************************************************
Test motif-in.meme.crp0.extdna.text ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.crp0.extdna.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.meme.crp0.extdna.html ...
SKIPPED!
*******************************************************************************
Generating dreme motifs...
dreme -oc results/motif.dreme.klf1 -m 2 -p common/Klf1-200-100.fa -n common/Klf1-200-100-shuffled.fa
sh: 1: /home/daria/meme-5.1.0/scripts/dreme: not found
*******************************************************************************
Test motif-in.dreme.klf1.text ...
SKIPPED!
*******************************************************************************
Test motif-in.dreme.klf1.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.dreme.klf1.html ...
SKIPPED!
*******************************************************************************
Generating dreme motifs...
dreme -oc results/motif.dreme.klf1.extdna -alph common/extended_dna.alph -m 2 -p common/Klf1-200-100.fa -n common/Klf1-200-100-shuffled.fa
sh: 1: /home/daria/meme-5.1.0/scripts/dreme: not found
*******************************************************************************
Test motif-in.dreme.klf1.extdna.text ...
SKIPPED!
*******************************************************************************
Test motif-in.dreme.klf1.extdna.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.dreme.klf1.extdna.html ...
SKIPPED!
*******************************************************************************
Generating dreme motifs...
dreme -oc results/motif.dreme.puf3p -rna -m 3 -p common/Puf3p.s
sh: 1: /home/daria/meme-5.1.0/scripts/dreme: not found
*******************************************************************************
Test motif-in.dreme.puf3p.text ...
SKIPPED!
*******************************************************************************
Test motif-in.dreme.puf3p.xml ...
SKIPPED!
*******************************************************************************
Test motif-in.dreme.puf3p.html ...
SKIPPED!
RUN: ama
========
*******************************************************************************
Test ama1 ...
ama --verbosity 1 --scoring max-odds gomo/motif.meme.txt gomo/seqs.fasta gomo/seqs.bg 1> results/ama1/ama_MDF_X_stdout 2> log
reference gomo/ama.withMaxodds.xml output results/ama1/ama_MDF_X_stdout
PASSED!
*******************************************************************************
Test ama2 ...
ama --pvalues --verbosity 1 --cs gomo/motif.meme.txt gomo/seqs_red.fasta gomo/seqs.norc.bg 1> results/ama2/ama_0PZsO_stdout 2> log
reference gomo/ama.redundant.xml output results/ama2/ama_0PZsO_stdout
PASSED!
RUN: ame
========
*******************************************************************************
Test ame1 ...
ame --verbose 1 --method fisher --scoring totalhits --oc results/ame1 --evalue-report-threshold 2 --hit-lo-fraction 0.85 --bgfile --uniform-- common/Klf1-200-100.combined.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame2 ...
ame --verbose 1 --method fisher --scoring totalhits --oc results/ame2 --evalue-report-threshold 2 --hit-lo-fraction 0.85 --bgfile --motif-- -motif-pseudo 0 --control --shuffle-- --seed 5 common/Klf1-200-100.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame3 ...
ame --verbose 1 --method fisher --scoring totalhits --oc results/ame3 --evalue-report-threshold 2 --hit-lo-fraction 0.85 --fix-partition 169 common/Klf1-200-100.combined.nofasta.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame4 ...
ame --verbose 1 --method fisher --scoring avg --oc results/ame4 --evalue-report-threshold 2 --bgfile --uniform-- --poslist fasta --hit-lo-fraction 0.85 common/Klf1-200-100.combined.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame5 ...
ame --verbose 1 --method fisher --scoring avg --oc results/ame5 --evalue-report-threshold 2 --bgfile --motif-- -motif-pseudo 0 --control --shuffle-- --kmer 1 common/Klf1-200-100.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame6 ...
ame --verbose 1 --method fisher --scoring avg --oc results/ame6 --evalue-report-threshold 2 --fix-partition 169 common/Klf1-200-100.combined.nofasta.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame7 ...
ame --verbose 1 --method ranksum --scoring totalhits --oc results/ame7 --evalue-report-threshold 100 --hit-lo-fraction 0.85 --bgfile --uniform-- common/Klf1-200-100.combined.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame8 ...
ame --verbose 1 --method ranksum --scoring totalhits --oc results/ame8 --evalue-report-threshold 100 --hit-lo-fraction 0.85 --bgfile --motif-- -motif-pseudo 0 --control common/Klf1-200-100-shuffled.fa common/Klf1-200-100.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame9 ...
ame --verbose 1 --method ranksum --scoring totalhits --oc results/ame9 --evalue-report-threshold 100 --hit-lo-fraction 0.85 --fix-partition 169 common/Klf1-200-100.combined.nofasta.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame10 ...
ame --verbose 1 --method ranksum --scoring avg --oc results/ame10 --evalue-report-threshold 100 --bgfile --uniform-- --poslist fasta --hit-lo-fraction 0.85 common/Klf1-200-100.combined.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame11 ...
ame --verbose 1 --method ranksum --scoring avg --oc results/ame11 --evalue-report-threshold 100 --bgfile --motif-- -motif-pseudo 0 --control common/Klf1-200-100-shuffled.fa common/Klf1-200-100.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame12 ...
ame --verbose 1 --method ranksum --scoring avg --oc results/ame12 --evalue-report-threshold 100 --fix-partition 169 common/Klf1-200-100.combined.nofasta.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test ame13 ...
ame --oc results/ame13 --verbose 1 --xalph common/dna_with_covalent.alph --inc MA00\* --inc MA04\* --exc MA007\* --inc T\* --bgfile common/dna_with_covalent.bg --kmer 1 --control --shuffle-- --motif-pseudo 1 common/dna_with_covalent.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme common/dna_with_covalent.meme &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
ame exited with value 139 indicating failure.
FAILED!
RUN: centrimo
=============
*******************************************************************************
Test centrimo1 ...
centrimo --verbosity 1 --oc results/centrimo1 --flip --motif-pseudo 1 common/Klf1.fa centrimo/dreme-Klf1.xml &> log
Failed to open html template file
reference centrimo/seq_bg_site_counts.txt output results/centrimo1/site_counts.txt
reference centrimo/seq_bg_centrimo.tsv output results/centrimo1/centrimo.tsv
-------------------------------------------------------------------------------
centrimo did not create the file "results/centrimo1/centrimo.html"
FAILED!
*******************************************************************************
Test centrimo2 ...
centrimo --verbosity 1 --oc results/centrimo2 --flip --bfile --motif-- --motif-pseudo 1 common/Klf1.fa centrimo/dreme-Klf1.xml &> log
Failed to open html template file
reference centrimo/motif_bg_site_counts.txt output results/centrimo2/site_counts.txt
reference centrimo/motif_bg_centrimo.tsv output results/centrimo2/centrimo.tsv
-------------------------------------------------------------------------------
centrimo did not create the file "results/centrimo2/centrimo.html"
FAILED!
*******************************************************************************
Test centrimo3 ...
centrimo --verbosity 1 --oc results/centrimo3 --flip --bfile --uniform-- --motif-pseudo 1 common/Klf1.fa centrimo/dreme-Klf1.xml &> log
Failed to open html template file
reference centrimo/uni_bg_site_counts.txt output results/centrimo3/site_counts.txt
reference centrimo/uni_bg_centrimo.tsv output results/centrimo3/centrimo.tsv
-------------------------------------------------------------------------------
centrimo did not create the file "results/centrimo3/centrimo.html"
FAILED!
*******************************************************************************
Test centrimo4 ...
centrimo --oc results/centrimo4 --verbosity 1 --cd --xalph common/dna_with_covalent.alph --noseq --inc MA00\* --inc MA04\* --exc MA007\* --inc T\* common/dna_with_covalent.fa common/Jaspar-subset.meme common/Jaspar-subset2.meme common/dna_with_covalent.meme &> log
Failed to open html template file
reference centrimo/dna_with_covalent_site_counts.txt output results/centrimo4/site_counts.txt
reference centrimo/dna_with_covalent_centrimo.tsv output results/centrimo4/centrimo.tsv
-------------------------------------------------------------------------------
centrimo did not create the file "results/centrimo4/centrimo.html"
FAILED!
*******************************************************************************
Test centrimo5 ...
centrimo --verbosity 1 --oc results/centrimo5 --neg common/Klf1-200.fa --motif-pseudo 1 common/Klf1.fa common/Jaspar-subset.meme &> log
Failed to open html template file
reference centrimo/neg_site_counts.txt output results/centrimo5/site_counts.txt
reference centrimo/neg_centrimo.tsv output results/centrimo5/centrimo.tsv
-------------------------------------------------------------------------------
centrimo did not create the file "results/centrimo5/centrimo.html"
FAILED!
*******************************************************************************
Test centrimo6 ...
centrimo --verbosity 1 --oc results/centrimo6 --cd -flip --motif-pseudo 1 --ethresh 1e-43 common/Klf1.fa centrimo/dreme-Klf1.xml &> log
Failed to open html template file
reference centrimo/cd_seq_bg_site_counts.txt output results/centrimo6/site_counts.txt
reference centrimo/cd_seq_bg_centrimo.tsv output results/centrimo6/centrimo.tsv
-------------------------------------------------------------------------------
centrimo did not create the file "results/centrimo6/centrimo.html"
FAILED!
*******************************************************************************
Test centrimo7 ...
centrimo --verbosity 1 --oc results/centrimo7 --ethresh 0.03 --local --sep --neg common/Klf1-200.fa --motif-pseudo 1 --bfile common/non-uniform.bg common/Klf1.fa common/Jaspar-subset.meme &> log
Failed to open html template file
reference centrimo/local_neg_site_counts.txt output results/centrimo7/site_counts.txt
reference centrimo/local_neg_centrimo.tsv output results/centrimo7/centrimo.tsv
-------------------------------------------------------------------------------
centrimo did not create the file "results/centrimo7/centrimo.html"
FAILED!
*******************************************************************************
Test centrimo8 ...
centrimo --verbosity 1 --oc results/centrimo8 --neg common/Klf1-200.fa --use-lo-fraction --motif-pseudo 1 common/Klf1.fa common/Jaspar-subset.meme &> log
Failed to open html template file
reference centrimo/neg_lo_site_counts.txt output results/centrimo8/site_counts.txt
reference centrimo/neg_lo_centrimo.tsv output results/centrimo8/centrimo.tsv
-------------------------------------------------------------------------------
centrimo did not create the file "results/centrimo8/centrimo.html"
FAILED!
*******************************************************************************
Test centrimo9 ...
centrimo --verbosity 1 --oc results/centrimo9 --neg common/Klf1-200.fa --use-pvalues --score 0.1 --motif-pseudo 1 common/Klf1.fa common/Jaspar-subset.meme &> log
Failed to open html template file
reference centrimo/neg_pv_site_counts.txt output results/centrimo9/site_counts.txt
reference centrimo/neg_pv_centrimo.tsv output results/centrimo9/centrimo.tsv
-------------------------------------------------------------------------------
9c9
< 1 MA0079.1 SP1 KRGGCDGGGT 8.5e-4 7.7e-5 -9.47 0.0 181.0 491 108 198 0.36864 3.2e-7 245 17 44 1.0e0 0.00 1.0e0 -0.00
---
> 1 MA0079.1 SP1 KRGGCDGGGT 8.5e-4 7.7e-5 -9.47 0.0 181.0 491 108 198 0.36864 3.2e-7 245 17 44 1.0e0 0.00 1.0e0 0.00
centrimo did not create the file "results/centrimo9/centrimo.html"
FAILED!
RUN: tgene
==========
*******************************************************************************
Test tgene1 ...
tgene -oc results/tgene1 tgene/P300.2x.bed tgene/gencode.v7.transcripts.chr21.gtf -max-link-distances 500000,1000 -tissues A549,Ag04450,Bj,Gm12878,H1hesc,Helas3,Hepg2,Huvec,K562,Mcf7,Nhek,Sknshra -histone-root tgene/Histone -histones H3k27ac,H3k4me3 -rna-source Cage -expression-root tgene/Expression -no-closest-locus -desc "Predicted links from P300 binding sites to genes on human chromosome 21" -verbosity 1 &> log
Failed to open html template file
reference tgene/p300_links.tsv output results/tgene1/links.tsv
-------------------------------------------------------------------------------
tgene did not create the file "results/tgene1/tgene.html"
FAILED!
*******************************************************************************
Test tgene2 ...
tgene -oc results/tgene2 tgene/P300.2x.bed tgene/gencode.v7.transcripts.chr21.gtf -max-link-distances 500000,1000 -tissues A549,Ag04450,Bj,Gm12878,H1hesc,Helas3,Hepg2,Hmec,Hsmm,Huvec,K562,Mcf7,Nhek,Nhlf,Sknshra -histone-root tgene/Histone -histones H3k27ac,H3k4me3 -rna-source Cage -expression-root tgene/Expression -no-closest-locus -desc "Predicted links from P300 binding sites to genes on human chromosome 21" -verbosity 1 &> log
Failed to open html template file
reference tgene/p300_links.tsv output results/tgene2/links.tsv
-------------------------------------------------------------------------------
tgene did not create the file "results/tgene2/tgene.html"
FAILED!
*******************************************************************************
Test tgene3 ...
tgene -oc results/tgene3 tgene/Rxra.bed tgene/gencode.v7.transcripts.chr21.gtf -max-link-distances 500000 -tissues A549,Ag04450,Bj,Gm12878,H1hesc,Helas3,Hepg2,Huvec,K562,Mcf7,Nhek,Sknshra -rna-source Cage -histone-root tgene/Histone -histones H3k27ac -rna-source Cage -expression-root tgene/Expression -no-closest-locus -no-closest-tss -desc "Predicted links from Rxra binding sites to genes on human chromosome 21 using H3k27ac only" -verbosity 1 &> log
Failed to open html template file
reference tgene/Rxra_links.tsv output results/tgene3/links.tsv
-------------------------------------------------------------------------------
tgene did not create the file "results/tgene3/tgene.html"
FAILED!
*******************************************************************************
Test tgene4 ...
tgene -oc results/tgene4 tgene/P300.2x.bed tgene/gencode.v7.transcripts.chr21.gtf -max-link-distances 500000 -no-closest-locus -desc "Predicted links from P300 binding sites to genes on human chromosome 21 w/o tissue panel" -verbosity 3 &> log
The output directory 'results/tgene4' already exists.
Its contents will be overwritten.
Reading locus file tgene/P300.2x.bed of putative regulatory elements.
Locus file contains 2676 entries.
Removing duplicate regulatory element locus: chr2:24238393-24238843
Removing duplicate regulatory element locus: chr2:26234842-26235800
Removing duplicate regulatory element locus: chr2:28021919-28022522
Removing duplicate regulatory element locus: chr2:30495973-30496739
Removing duplicate regulatory element locus: chr2:30497388-30498100
Removing duplicate regulatory element locus: chr2:30523453-30524041
Removing duplicate regulatory element locus: chr2:36624947-36625626
Removing duplicate regulatory element locus: chr2:36630749-36631433
Removing duplicate regulatory element locus: chr2:42157922-42158452
Removing duplicate regulatory element locus: chr2:42161576-42162039
Removing duplicate regulatory element locus: chr2:44518282-44519021
Removing duplicate regulatory element locus: chr2:46542394-46542880
Removing duplicate regulatory element locus: chr2:47082241-47082973
Removing duplicate regulatory element locus: chr2:47403669-47404015
Removing duplicate regulatory element locus: chr2:56066257-56066711
Removing duplicate regulatory element locus: chr2:62796997-62797771
Removing duplicate regulatory element locus: chr2:67788483-67789212
Removing duplicate regulatory element locus: chr2:70008432-70009022
Removing duplicate regulatory element locus: chr2:72498879-72499731
Removing duplicate regulatory element locus: chr2:85648412-85648941
Removing duplicate regulatory element locus: chr2:86120898-86121424
Removing duplicate regulatory element locus: chr2:101741305-101741923
Removing duplicate regulatory element locus: chr2:107618754-107619177
Removing duplicate regulatory element locus: chr2:107642130-107642947
Removing duplicate regulatory element locus: chr2:110863416-110864165
Removing duplicate regulatory element locus: chr2:113998401-113998986
Removing duplicate regulatory element locus: chr2:138817689-138818184
Removing duplicate regulatory element locus: chr2:138829744-138830278
Removing duplicate regulatory element locus: chr2:150845919-150846404
Removing duplicate regulatory element locus: chr2:161417979-161418392
Removing duplicate regulatory element locus: chr2:164524016-164524415
Removing duplicate regulatory element locus: chr2:173867800-173868253
Removing duplicate regulatory element locus: chr2:173913553-173914375
Removing duplicate regulatory element locus: chr2:173913553-173914375
Removing duplicate regulatory element locus: chr2:175837020-175837430
Removing duplicate regulatory element locus: chr2:178131050-178131609
Removing duplicate regulatory element locus: chr2:188394738-188395172
Removing duplicate regulatory element locus: chr2:191906420-191907072
Removing duplicate regulatory element locus: chr2:191914596-191915690
Removing duplicate regulatory element locus: chr2:192036269-192036961
Removing duplicate regulatory element locus: chr2:192084034-192084612
Removing duplicate regulatory element locus: chr2:196385234-196385981
Removing duplicate regulatory element locus: chr2:201612764-201613273
Removing duplicate regulatory element locus: chr2:206565205-206565907
Removing duplicate regulatory element locus: chr2:211413613-211414144
Removing duplicate regulatory element locus: chr2:221093351-221093881
Removing duplicate regulatory element locus: chr2:221142110-221142799
Removing duplicate regulatory element locus: chr2:226979756-226980240
Removing duplicate regulatory element locus: chr2:226983143-226984266
Removing duplicate regulatory element locus: chr2:227342723-227343457
Removing duplicate regulatory element locus: chr2:228682786-228683880
Removing duplicate regulatory element locus: chr2:228682786-228683880
Removing duplicate regulatory element locus: chr2:234322151-234322954
Removing duplicate regulatory element locus: chr2:234395504-234396432
Removing duplicate regulatory element locus: chr2:234616587-234617246
Removing duplicate regulatory element locus: chr2:235166835-235167329
Removing duplicate regulatory element locus: chr2:235271524-235272157
Removing duplicate regulatory element locus: chr2:236007458-236007964
Removing duplicate regulatory element locus: chr2:239348080-239348489
Removing duplicate regulatory element locus: chr2:239592945-239594073
Removing duplicate regulatory element locus: chr2:239592945-239594073
Removing duplicate regulatory element locus: chr2:241327024-241327413
Removing duplicate regulatory element locus: chr20:10231398-10232057
Removing duplicate regulatory element locus: chr20:11188384-11189027
Removing duplicate regulatory element locus: chr20:11367729-11368355
Removing duplicate regulatory element locus: chr20:14859629-14860404
Removing duplicate regulatory element locus: chr20:14966617-14967287
Removing duplicate regulatory element locus: chr20:22384503-22385026
Removing duplicate regulatory element locus: chr20:22451133-22451545
Removing duplicate regulatory element locus: chr20:30196049-30196807
Removing duplicate regulatory element locus: chr20:30300411-30300945
Removing duplicate regulatory element locus: chr20:36007148-36007949
Removing duplicate regulatory element locus: chr20:36008692-36009296
Removing duplicate regulatory element locus: chr20:36738281-36738821
Removing duplicate regulatory element locus: chr20:43023107-43023572
Removing duplicate regulatory element locus: chr20:43321557-43322071
Removing duplicate regulatory element locus: chr20:45988851-45989313
Removing duplicate regulatory element locus: chr20:46081864-46082401
Removing duplicate regulatory element locus: chr20:48384723-48385508
Removing duplicate regulatory element locus: chr20:48909048-48909559
Removing duplicate regulatory element locus: chr20:48925055-48925685
Removing duplicate regulatory element locus: chr20:50527130-50527698
Removing duplicate regulatory element locus: chr20:52390198-52390995
Removing duplicate regulatory element locus: chr20:52724015-52724768
Removing duplicate regulatory element locus: chr20:52757372-52758023
Removing duplicate regulatory element locus: chr20:52765423-52766015
Removing duplicate regulatory element locus: chr20:55358835-55359349
Removing duplicate regulatory element locus: chr20:56273258-56273802
Removing duplicate regulatory element locus: chr20:56323549-56324068
Removing duplicate regulatory element locus: chr20:56592236-56593268
Removing duplicate regulatory element locus: chr20:56592236-56593268
Removing duplicate regulatory element locus: chr20:61863466-61864363
Removing duplicate regulatory element locus: chr21:16816380-16817396
Removing duplicate regulatory element locus: chr21:16816380-16817396
Removing duplicate regulatory element locus: chr21:38255995-38256567
Removing duplicate regulatory element locus: chr21:39511717-39512242
Removing duplicate regulatory element locus: chr21:39649445-39650105
Removing duplicate regulatory element locus: chr21:44753165-44753648
Removing duplicate regulatory element locus: chr21:44860419-44861441
Removing duplicate regulatory element locus: chr21:44936643-44937264
Removing duplicate regulatory element locus: chr21:45132033-45132841
Removing duplicate regulatory element locus: chr22:30591744-30593090
Removing duplicate regulatory element locus: chr22:30601360-30602148
Removing duplicate regulatory element locus: chr22:30602889-30603428
Removing duplicate regulatory element locus: chr22:30608414-30608975
Removing duplicate regulatory element locus: chr22:35985167-35985852
Removing duplicate regulatory element locus: chr22:40894380-40894991
Removing duplicate regulatory element locus: chr22:40905605-40906153
Removing duplicate regulatory element locus: chr22:45999977-46000616
Removing duplicate regulatory element locus: chr22:46034673-46035548
Removing duplicate regulatory element locus: chr22:46173094-46173754
Removing duplicate regulatory element locus: chr22:48765760-48766512
Locus table contains 2564 valid entries (0 duplicates removed).
Reading the annotation file 'tgene/gencode.v7.transcripts.chr21.gtf'.
The annotation file contained 2183 entries.
Creating the transcript table with 2183 entries.
Removing transcripts for invalid transcript types from the table.
Transcript table now contains 1600 transcripts (583 removed).
Creating the link table based on distance alone.
Distance: 500000
Finding the closest loci to each TSS and creating links.
Finding the closest TSS(es) to each locus.
Created 8772 links.
Computing p-values and q-values for 8772 links
Estimated 8772 Distance p-values.
Converting Distance p-values to q-values.
Estimating pi_0 from all 8772 observed p-values.
Estimating pi_0.
Minimal pi_zero = 0.997405
Estimated pi_0=0.997922
Failed to open html template file
Program ends correctly.
reference tgene/p300_no_panel_links.tsv output results/tgene4/links.tsv
-------------------------------------------------------------------------------
tgene did not create the file "results/tgene4/tgene.html"
FAILED!
RUN: create_priors
==================
*******************************************************************************
Test create-priors1 ...
create-priors -oc results/create-priors1 create-priors/chrX.fa create-priors/DNaseHS_gm12878.wig &> log
Program create-priors not found!
SKIPPED!
*******************************************************************************
Test create-priors2 ...
create-priors -oc results/create-priors2 create-priors/chrX.fa create-priors/DNaseHS_gm12878.wig &> log
Program create-priors not found!
SKIPPED!
RUN: dreme
==========
*******************************************************************************
Test dreme1 ...
dreme -oc results/dreme1 -verbosity 1 -p common/Klf1-200-100.fa -n common/Klf1-200-100-shuffled.fa &> log
Program dreme not found!
SKIPPED!
*******************************************************************************
Test dreme2 ...
dreme -norc -oc results/dreme2 -verbosity 1 -p common/Klf1-200-100.fa -n common/Klf1-200-100-shuffled.fa &> log
Program dreme not found!
SKIPPED!
*******************************************************************************
Test dreme3 ...
dreme-py3 -oc results/dreme3 -verbosity 1 -p common/Klf1-200-100.fa -n common/Klf1-200-100-shuffled.fa &> log
Program dreme-py3 not found!
SKIPPED!
*******************************************************************************
Test dreme4 ...
dreme-py3 -norc -oc results/dreme4 -verbosity 1 -p common/Klf1-200-100.fa -n common/Klf1-200-100-shuffled.fa &> log
Program dreme-py3 not found!
SKIPPED!
RUN: fasta-center
=================
*******************************************************************************
Test fasta-center1 ...
fasta-center -len 100 -dna < common/Klf1-200.fa 1> results/fasta-center1/fasta-center_wJ6aI_stdout 2> log
Program fasta-center not found!
SKIPPED!
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_N_ozB_stdout 2> log
Program fasta-dinucleotide-shuffle not found!
SKIPPED!
RUN: fimo
=========
*******************************************************************************
Test fimo1 ...
fimo --oc results/fimo1 --motif-pseudo 0.01 fimo/MCM1.meme.html fimo/spiked.fasta &> log
Using motif +TTTCCYDWTTBGGAAATW of width 18.
Using motif -TTTCCYDWTTBGGAAATW of width 18.
Computing q-values.
Estimating pi_0 from a uniformly sampled set of 5298 p-values.
Estimating pi_0.
Estimated pi_0=0.799106
reference fimo/fimo.tsv output results/fimo1/fimo.tsv
PASSED!
*******************************************************************************
Test fimo2 ...
fimo --oc results/fimo2 --motif CGGYGGGG --motif GCATCRGRBSAGA --no-qvalue --thresh 0.01 common/crp0.meme.xml 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 fimo/fimo-motif23.tsv output results/fimo2/fimo.tsv
PASSED!
*******************************************************************************
Test fimo3 ...
fimo --oc results/fimo3 --psp fimo/GCN4_YPD.psp --prior-dist fimo/prior.dist.txt fimo/GCN4.meme.txt fimo/GCN4_YPD.fasta &> log
Using motif +MA0303.1 of width 21.
Using motif -MA0303.1 of width 21.
Computing q-values.
Estimating pi_0 from a uniformly sampled set of 10000 p-values.
Estimating pi_0.
Estimated pi_0=1
reference fimo/fimo-priors.tsv output results/fimo3/fimo.tsv
PASSED!
*******************************************************************************
Test fimo4 ...
fimo --oc results/fimo4 --parse-genomic-coord --psp fimo/GCN4_YPD-genomic.psp --prior-dist fimo/prior.dist.txt fimo/GCN4.meme.txt fimo/GCN4_YPD-genomic.fasta &> log
Using motif +MA0303.1 of width 21.
Using motif -MA0303.1 of width 21.
Computing q-values.
Estimating pi_0 from a uniformly sampled set of 10000 p-values.
Estimating pi_0.
Estimated pi_0=1
reference fimo/fimo-priors-genomic.tsv output results/fimo4/fimo.tsv
PASSED!
RUN: glam2
==========
*******************************************************************************
Test glam2_1 ...
glam2 -M -r 3 -n 100 -O results/glam2_1 p common/At.s &> log
The output directory 'results/glam2_1' already exists.
Its contents will be overwritten.
Run 1... 406 iterations
Run 2... 445 iterations
Run 3... 400 iterations
Warning: could not find glam2html script! Failed to convert output to HTML!
Warning: could not find glam2psfm script! Failed to convert to MEME format motif!
-------------------------------------------------------------------------------
glam2 exited with value 1 indicating failure.
FAILED!
RUN: glam2scan
==============
*******************************************************************************
Test glam2scan1 ...
glam2scan -O results/glam2scan1 p glam2/glam2.txt common/At.s &> log
The output directory 'results/glam2scan1' already exists.
Its contents will be overwritten.
Warning: could not find glam2scan2html script! Failed to convert output to HTML!
-------------------------------------------------------------------------------
glam2scan exited with value 1 indicating failure.
FAILED!
RUN: gomo
=========
*******************************************************************************
Test gomo1 ...
gomo --seed 1 --nostatus --verbosity 1 --oc results/gomo1 --motifs gomo/motif.meme.txt gomo/GO2Gene.map.csv gomo/ama.nozscoring.xml &> log
-------------------------------------------------------------------------------
gomo exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test gomo2 ...
gomo --gs --seed 1 --nostatus --verbosity 1 --oc results/gomo2 --motifs gomo/motif.meme.txt gomo/GO2Gene.map.csv gomo/ama.zscoring.xml gomo/ama.nozscoring.xml &> log
-------------------------------------------------------------------------------
gomo exited with value 1 indicating failure.
FAILED!
RUN: mast
=========
*******************************************************************************
Test mast1 ...
mast meme/meme.crp0.classic.oops.txt common/crp0.s -oc results/mast1 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.crp0.classic.oops.txt.xml output results/mast1/mast.xml
PASSED!
*******************************************************************************
Test mast2 ...
mast meme/meme.crp0.classic.zoops.xml common/crp0.s -oc results/mast2 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.crp0.classic.zoops.xml.xml output results/mast2/mast.xml
PASSED!
*******************************************************************************
Test mast3 ...
mast meme/meme.crp0.classic.anr.html common/crp0.s -oc results/mast3 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.crp0.classic.anr.html.xml output results/mast3/mast.xml
PASSED!
*******************************************************************************
Test mast4 ...
mast meme/meme.INO_up800.classic.oops.txt common/INO_up800.s -oc results/mast4 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.INO_up800.classic.oops.txt.xml output results/mast4/mast.xml
PASSED!
*******************************************************************************
Test mast5 ...
mast meme/meme.INO_up800.classic.zoops.xml common/INO_up800.s -oc results/mast5 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.INO_up800.classic.zoops.xml.xml output results/mast5/mast.xml
PASSED!
*******************************************************************************
Test mast6 ...
mast meme/meme.INO_up800.classic.anr.html common/INO_up800.s -oc results/mast6 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.INO_up800.classic.anr.html.xml output results/mast6/mast.xml
PASSED!
*******************************************************************************
Test mast7 ...
mast meme/meme.farntrans5.classic.oops.txt common/farntrans5.s -oc results/mast7 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.farntrans5.classic.oops.txt.xml output results/mast7/mast.xml
PASSED!
*******************************************************************************
Test mast8 ...
mast meme/meme.farntrans5.classic.zoops.xml common/farntrans5.s -oc results/mast8 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.farntrans5.classic.zoops.xml.xml output results/mast8/mast.xml
PASSED!
*******************************************************************************
Test mast9 ...
mast meme/meme.farntrans5.classic.anr.html common/farntrans5.s -oc results/mast9 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.farntrans5.classic.anr.html.xml output results/mast9/mast.xml
PASSED!
*******************************************************************************
Test mast10 ...
mast meme/meme.lipocalin.classic.oops.txt common/lipocalin.s -oc results/mast10 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.lipocalin.classic.oops.txt.xml output results/mast10/mast.xml
PASSED!
*******************************************************************************
Test mast11 ...
mast meme/meme.lipocalin.classic.zoops.xml common/lipocalin.s -oc results/mast11 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.lipocalin.classic.zoops.xml.xml output results/mast11/mast.xml
PASSED!
*******************************************************************************
Test mast12 ...
mast meme/meme.lipocalin.classic.anr.html common/lipocalin.s -oc results/mast12 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.lipocalin.classic.anr.html.xml output results/mast12/mast.xml
PASSED!
*******************************************************************************
Test mast13 ...
mast meme/meme.adh.classic.oops.txt common/adh.s -oc results/mast13 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.adh.classic.oops.txt.xml output results/mast13/mast.xml
PASSED!
*******************************************************************************
Test mast14 ...
mast meme/meme.adh.classic.oops.txt - -oc results/mast14 -nostatus -df stdin -dna -seqp < common/mini-drosoph.s &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.adh.classic.oops.mini-drosoph.txt.xml output results/mast14/mast.xml
PASSED!
*******************************************************************************
Test mast15 ...
mast meme/meme.adh.classic.zoops.html common/adh.s -oc results/mast15 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.adh.classic.zoops.html.xml output results/mast15/mast.xml
PASSED!
*******************************************************************************
Test mast16 ...
mast meme/meme.adh.classic.zoops.html - -oc results/mast16 -nostatus -df stdin -dna -seqp < common/mini-drosoph.s &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.adh.classic.zoops.mini-drosoph.html.xml output results/mast16/mast.xml
PASSED!
*******************************************************************************
Test mast17 ...
mast meme/meme.adh.classic.anr.xml common/adh.s -oc results/mast17 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.adh.classic.anr.xml.xml output results/mast17/mast.xml
PASSED!
*******************************************************************************
Test mast18 ...
mast meme/meme.adh.classic.anr.xml - -oc results/mast18 -nostatus -df stdin -dna -seqp < common/mini-drosoph.s &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
reference mast/mast.adh.classic.anr.mini-drosoph.xml.xml output results/mast18/mast.xml
PASSED!
*******************************************************************************
Test mast19 ...
mast meme/meme.INO_up800.classic.anr.txt common/INO_up800.s -oc results/mast19 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
-------------------------------------------------------------------------------
mast did not create the file "results/mast19/mast.html"
FAILED!
*******************************************************************************
Test mast20 ...
mast meme/meme.INO_up800.classic.anr.xml common/INO_up800.s -oc results/mast20 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
-------------------------------------------------------------------------------
mast did not create the file "results/mast20/mast.html"
FAILED!
*******************************************************************************
Test mast21 ...
mast meme/meme.INO_up800.classic.anr.html common/INO_up800.s -oc results/mast21 -nostatus &> log
Warning: could not find mast_xml_to_html. The HTML output could not be created.
Warning: could not find mast_xml_to_txt. The text output could not be created.
-------------------------------------------------------------------------------
mast did not create the file "results/mast21/mast.html"
FAILED!
RUN: mcast
==========
*******************************************************************************
Test mcast1 ...
mcast -oc results/mcast1 meme/meme.lex0.zoops.txt common/lex0.s &> log
Creating HMM from motif array.
Building HMM: (0) 1 2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21 | 22-23-24-25-26-27-28-29-30-31-32-33-34-35-36-37-38-39-40-41 | (42)
Reading sequences in blocks of 232558 characters.
Warning: Cannot estimate pi_0 accurately from fewer than 100 p-values. total p-values = 14. Using pi_zero = 1.0.
User time for computation: 0.002363 seconds
System time for computation: 0 seconds
Failed to open html template file /home/daria/meme-5.1.0/etc/mcast_template.html.
User time for output: 0.000125 seconds
System time for output: 0 seconds
Total user time: 0.002488 seconds
Total system time: 0 seconds
reference mcast/lex0.zoops.tsv output results/mcast1/mcast.tsv
reference mcast/lex0.zoops.gff output results/mcast1/mcast.gff
reference mcast/lex0.zoops.xml output results/mcast1/mcast.xml
reference mcast/lex0.zoops.cisml output results/mcast1/cisml.xml
-------------------------------------------------------------------------------
mcast did not create the file "results/mcast1/mcast.html"
FAILED!
*******************************************************************************
Test mcast2 ...
mcast -oc results/mcast2 -parse-genomic-coord fimo/GCN4.meme.txt fimo/GCN4_YPD-genomic.fasta &> log
Creating HMM from motif array.
Building HMM: (0) 1 2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22 | 23-24-25-26-27-28-29-30-31-32-33-34-35-36-37-38-39-40-41-42-43 | (44)
Reading sequences in blocks of 222222 characters.
Warning: Cannot estimate pi_0 accurately from fewer than 100 p-values. total p-values = 34. Using pi_zero = 1.0.
User time for computation: 0.007069 seconds
System time for computation: 0 seconds
Failed to open html template file /home/daria/meme-5.1.0/etc/mcast_template.html.
User time for output: 0.000114 seconds
System time for output: 0 seconds
Total user time: 0.007183 seconds
Total system time: 0 seconds
reference mcast/parse_genomic.tsv output results/mcast2/mcast.tsv
reference mcast/parse_genomic.gff output results/mcast2/mcast.gff
reference mcast/parse_genomic.xml output results/mcast2/mcast.xml
reference mcast/parse_genomic.cisml output results/mcast2/cisml.xml
-------------------------------------------------------------------------------
mcast did not create the file "results/mcast2/mcast.html"
FAILED!
RUN: meme
=========
*******************************************************************************
Test meme1 ...
meme -p 5 common/crp0.s -oc results/meme1 -mod oops -dna -revcomp -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme2 ...
meme -p 5 -minsites 3 -maxsites 17 common/crp0.s -oc results/meme2 -mod zoops -dna -revcomp -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme3 ...
meme -p 5 -minsites 3 -maxsites 17 common/crp0.s -oc results/meme3 -mod anr -dna -revcomp -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme4 ...
meme -p 5 common/adh.s -oc results/meme4 -mod oops -protein -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme5 ...
meme -p 5 -nsites 27 common/adh.s -oc results/meme5 -mod zoops -protein -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme6 ...
meme -p 5 -nsites 27 common/adh.s -oc results/meme6 -mod anr -protein -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme7 ...
meme -p 5 -csites 30 common/Klf1-200-100.fa -oc results/meme7 -mod oops -dna -revcomp -brief 0 -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme8 ...
meme -p 5 -csites 30 common/Klf1-200-100.fa -oc results/meme8 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme9 ...
meme -p 5 -csites 30 common/Klf1-200-100.fa -oc results/meme9 -mod anr -dna -revcomp -brief 0 -nmotifs 2 -objfun classic -minw 8 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme10 ...
meme -p 5 common/crp0.s -oc results/meme10 -mod oops -dna -revcomp -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme11 ...
meme -p 5 -minsites 3 -maxsites 17 common/crp0.s -oc results/meme11 -mod zoops -dna -revcomp -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme12 ...
meme -p 5 -minsites 3 -maxsites 17 common/crp0.s -oc results/meme12 -mod anr -dna -revcomp -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme13 ...
meme -p 5 common/adh.s -oc results/meme13 -mod oops -protein -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme14 ...
meme -p 5 -nsites 27 common/adh.s -oc results/meme14 -mod zoops -protein -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme15 ...
meme -p 5 -nsites 27 common/adh.s -oc results/meme15 -mod anr -protein -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme16 ...
meme -p 5 common/Klf1-200-100.fa -oc results/meme16 -mod oops -dna -revcomp -brief 0 -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme17 ...
meme -p 5 common/Klf1-200-100.fa -oc results/meme17 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme18 ...
meme -p 5 common/Klf1-200-100.fa -oc results/meme18 -mod anr -dna -revcomp -brief 0 -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus &> log
Program meme not found!
SKIPPED!
*******************************************************************************
Test meme_psp ...
meme -p 5 common/psp_test.s -oc results/meme19 -psp common/psp_test.psp -minsites 5 -dna -revcomp -minw 7 -maxw 12 -nostatus -searchsize 0 &> log
Program meme not found!
SKIPPED!
RUN: meme-chip
==============
*******************************************************************************
Test meme-chip1 ...
meme-chip -oc results/meme-chip1 -db meme-chip/JASPAR_CORE_2014_vertebrates.meme meme-chip/Klf1.100.fa &> log
Program meme-chip not found!
SKIPPED!
RUN: momo
=========
*******************************************************************************
Test momo1 ...
momo simple --oc results/momo1 --sequence-column sequence momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo2 ...
momo simple --oc results/momo2 --psm-type tide --protein-database momo/small-yeast.fasta --width 11 momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo3 ...
momo simple --oc results/momo3 --psm-type tide --single-motif-per-mass momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo4 ...
momo simple --oc results/momo4 --psm-type tide --protein-database momo/small-yeast.fasta --width 11 --hash-fasta 0 momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo5 ...
momo simple --oc results/momo5 --psm-type tide --eliminate-repeats 3 --protein-database momo/small-yeast.fasta momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo6 ...
momo simple --oc results/momo6 --psm-type tide --eliminate-repeats 0 momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo7 ...
momo simple --oc results/momo7 --psm-type tide --filter "xcorr rank,le,3" momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo8 ...
momo simple --oc results/momo8 --protein-database momo/small-yeast.fasta momo/small-tide-mod-phospho.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo9 ...
momo simple --oc results/momo9 --protein-database momo/small-yeast.fasta momo/small-tide-mod-phospho.fasta &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo10 ...
momo simple --oc results/momo10 --psm-type tide momo/small-tide-mod-1-out-of-2.txt momo/small-tide-mod-2-out-of-2.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo11 ...
momo motifx --oc results/momo11 --psm-type tide --protein-database momo/small-yeast.fasta --score-threshold 0.05 --min-occurrences 1 --harvard --seed 273 momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo12 ...
momo motifx --oc results/momo12 --psm-type tide --db-background --protein-database momo/small-yeast.fasta --score-threshold 0.05 --min-occurrences 1 --single-motif-per-mass --harvard momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo13 ...
momo motifx --oc results/momo13 --db-background --protein-database momo/small-yeast.fasta --score-threshold 0.05 --min-occurrences 1 momo/small-tide-mod-phospho.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo14 ...
momo motifx --oc results/momo14 --db-background --protein-database momo/small-yeast-prealigned-no-unknowns.txt --score-threshold 0.05 --min-occurrences 1 momo/small-tide-mod-phospho.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo15 ...
momo simple --oc results/momo15 --psm-type ms-gf+ --sequence-column Peptide momo/small-msgf-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo16 ...
momo simple --oc results/momo16 --psm-type comet --sequence-column "modified sequence" momo/small-comet-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo17 ...
momo modl --oc results/momo17 --psm-type tide --protein-database momo/small-yeast.fasta momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
*******************************************************************************
Test momo18 ...
momo modl --oc results/momo18 --psm-type tide --db-background --remove-unknowns T --protein-database momo/small-yeast.fasta momo/small-tide-mod.txt &> log
Failed to open HTML template file.
Segmentation fault (core dumped)
-------------------------------------------------------------------------------
momo exited with value 139 indicating failure.
FAILED!
RUN: motiph
===========
*******************************************************************************
Test motiph1 ...
motiph --seed 0 --bg 2 --pseudocount 0.01 --oc results/motiph1 motiph/spiked.aln motiph/yeast.tree motiph/MCM1.meme.html &> log
Program motiph not found!
SKIPPED!
*******************************************************************************
Test motiph2 ...
motiph --seed 0 --bg 2 --pseudocount 0.01 --oc results/motiph2 --output-pthresh 1 --motif CGGYGGGG --motif GCATCRGRBSAGA motiph/spiked.aln motiph/yeast.tree common/crp0.meme.html &> log
Program motiph not found!
SKIPPED!
RUN: pspgen
===========
*******************************************************************************
Test psp-gen1 ...
psp-gen -revcomp -pos psp-gen/one-peak-dna.fasta -neg psp-gen/all-A.fasta 1> results/pspgen1/psp-gen_P3QNY_stdout 2> log
Program psp-gen not found!
SKIPPED!
*******************************************************************************
Test psp-gen2 ...
psp-gen -protein -maxrange -triples -pos psp-gen/one-peak-protein.fasta -neg psp-gen/all-A.fasta 1> results/pspgen2/psp-gen_BNtXQ_stdout 2> log
Program psp-gen not found!
SKIPPED!
*******************************************************************************
Test psp-gen3 ...
psp-gen -alph common/extended_dna.alph -revcomp -pos psp-gen/one-peak-dna.fasta -neg psp-gen/all-A.fasta 1> results/pspgen1/psp-gen_wquC8_stdout 2> log
Program psp-gen not found!
SKIPPED!
RUN: qvalue
===========
*******************************************************************************
Test qvalue1 ...
qvalue --header 1 --append --column 2 --seed 7718 qvalue/uniform.txt 1> results/qvalue1/qvalue_rkZ8l_stdout 2> log
Program qvalue not found!
SKIPPED!
*******************************************************************************
Test qvalue2 ...
qvalue --null qvalue/null.txt qvalue/observed.txt 1> results/qvalue2/qvalue_4LP0s_stdout 2> log
Program qvalue not found!
SKIPPED!
RUN: spamo
==========
*******************************************************************************
Test spamo1 ...
spamo -oc results/spamo1 -verbosity 1 -margin 20 -shared 1 -bgfile --uniform-- spamo/limits.fasta spamo/primary.meme spamo/secondary.meme &> log
Failed to open html template file.
-------------------------------------------------------------------------------
spamo did not create the file "results/spamo1/spamo.html"
reference spamo/limits.tsv output results/spamo1/spamo.tsv
FAILED!
*******************************************************************************
Test spamo2 ...
spamo -oc results/spamo2 -verbosity 1 -margin 20 -shared 1 -bgfile --motif-- spamo/random.fasta spamo/primary.meme spamo/secondary.meme &> log
Failed to open html template file.
-------------------------------------------------------------------------------
spamo did not create the file "results/spamo2/spamo.html"
reference spamo/random.tsv output results/spamo2/spamo.tsv
FAILED!
*******************************************************************************
Test spamo3 ...
spamo -oc results/spamo3 -verbosity 3 -xalph -primary TGCm1C -keepprimary -margin 20 -shared 1 -inc MA00\* -inc T\* -exc MA007\* common/dna_with_covalent.fa common/dna_with_covalent.meme common/Jaspar-subset.meme common/dna_with_covalent.meme common/dna_with_covalent.meme &> log
The output directory 'results/spamo3' already exists.
Its contents will be overwritten.
Loading Primary Motif (name=TGCm1C)
Loading All Sequences
Loaded 2499 Sequences
Determining Best Primary Matches
Eliminating Sequences Without Primary Matches
Eliminated 1553 Sequences Without Primary Match
Trimming Sequences
Freeing Unneeded Sequences
Loading Secondary Motifs from file 'common/Jaspar-subset.meme'
Discarding motif 'MA0140.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.
Discarding motif 'MA0079.1' in 'common/Jaspar-subset.meme' it matched an -exc pattern.
Discarding motif 'MA0079.2' in 'common/Jaspar-subset.meme' it matched an -exc pattern.
Discarding motif 'MA0163.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.
Discarding motif 'MA0270.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.
Discarding motif 'MA0300.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.
Discarding motif 'MA0309.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.
Discarding motif 'MA0443.1' in 'common/Jaspar-subset.meme' because it did not match any -inc pattern.
Loading Secondary Motifs from file 'common/dna_with_covalent.meme'
Discarding motif 'CCTTCC' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'GCAGCA' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'GCAm1C' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'GCAm7C' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'GCm1C1' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'Gm1TGC' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'Gm7GCA' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'TGCmGC' in file 'common/dna_with_covalent.meme' (non-unique ID).
Warning: The following secondary motifs in 'common/dna_with_covalent.meme' were excluded as they didn't fit in the margin:
Tm1m1m1m1m1m1m1m1m1m1m1m1
Loading Secondary Motifs from file 'common/dna_with_covalent.meme'
Discarding motif 'CCTTCC' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'GCAGCA' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'GCAm1C' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'GCAm7C' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'GCm1C1' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'Gm1TGC' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'Gm7GCA' in 'common/dna_with_covalent.meme' because it did not match any -inc pattern.
Discarding motif 'TGCmGC' in file 'common/dna_with_covalent.meme' (non-unique ID).
Warning: The following duplicate secondary motifs in 'common/dna_with_covalent.meme' were excluded:
TGCmGC TGCm1C
Warning: The following secondary motifs in 'common/dna_with_covalent.meme' were excluded as they didn't fit in the margin:
Tm1m1m1m1m1m1m1m1m1m1m1m1
Scanning For Secondary Matches
Scanned 20%
Scanned 40%
Scanned 60%
Scanned 80%
Scanned 100%
Sorting Significant Secondary Motifs
Grouping Redundant Secondary Motifs
Outputting TSV
Failed to open html template file.
run_time cpu= 0.08 real= 0.00
-------------------------------------------------------------------------------
spamo did not create the file "results/spamo3/spamo.html"
reference spamo/dna_with_covalent.tsv output results/spamo3/spamo.tsv
FAILED!
*******************************************************************************
Test spamo4 ...
spamo -oc results/spamo4 -verbosity 1 -margin 20 -shared 1 -bgfile --uniform-- -dumpseqs -primary MA0039.2 -keepprimary -inc MA0039.2 -inc MA0140.1 common/Klf1.fa common/Jaspar-subset.meme common/Jaspar-subset.meme &> log
Failed to open html template file.
-------------------------------------------------------------------------------
spamo did not create the file "results/spamo4/spamo.html"
reference spamo/dumpseqs.tsv output results/spamo4/spamo.tsv
reference spamo/dumpseqs.seqs_MA0039.2_db1_MA0039.2.tsv output results/spamo4/seqs_MA0039.2_db1_MA0039.2.tsv
reference spamo/dumpseqs.seqs_MA0039.2_db1_MA0140.1.tsv output results/spamo4/seqs_MA0039.2_db1_MA0140.1.tsv
FAILED!
RUN: tomtom
===========
*******************************************************************************
Test tomtom1 ...
tomtom -oc results/tomtom1 -verbosity 1 -evalue -thresh 10 -m TGCm1C -mi 3 -xalph -bfile common/dna_with_covalent.bg -dist allr common/dna_with_covalent.meme common/dna_with_covalent.meme common/Jaspar-subset.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_allr ...
tomtom -verbosity 1 -dist allr -oc results/tomtom2 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_ed ...
tomtom -verbosity 1 -dist ed -oc results/tomtom3 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_kullback ...
tomtom -verbosity 1 -dist kullback -oc results/tomtom4 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_pearson ...
tomtom -verbosity 1 -dist pearson -oc results/tomtom5 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_sandelin ...
tomtom -verbosity 1 -dist sandelin -oc results/tomtom6 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_blic1 ...
tomtom -verbosity 1 -dist blic1 -oc results/tomtom7 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_blic5 ...
tomtom -verbosity 1 -dist blic5 -oc results/tomtom8 -incomplete-scores common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_allr_cs ...
tomtom -verbosity 1 -dist allr -oc results/tomtom9 common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_ed_cs ...
tomtom -verbosity 1 -dist ed -oc results/tomtom10 common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_kullback_cs ...
tomtom -verbosity 1 -dist kullback -oc results/tomtom11 common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_pearson_cs ...
tomtom -verbosity 1 -dist pearson -oc results/tomtom12 common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_sandelin_cs ...
tomtom -verbosity 1 -dist sandelin -oc results/tomtom13 common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_blic1_cs ...
tomtom -verbosity 1 -dist blic1 -oc results/tomtom14 common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test tomtom_blic5_cs ...
tomtom -verbosity 1 -dist blic5 -oc results/tomtom15 common/sample.meme common/sample.meme &> log
Warning: could not find tomtom_xml_to_html. The HTML output could not be created.
-------------------------------------------------------------------------------
tomtom exited with value 1 indicating failure.
FAILED!
I would be glad if someone could give advice
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