Failed

edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImplTest.ciccarelliTreeIsConvertedToTaxIdTree (from TestSuite)

Failing for the past 5 builds (Since #1 )
Took 0.28 sec.

Stacktrace

java.lang.NullPointerException
	at edu.berkeley.compbio.ncbitaxonomy.NcbiTaxonomyPhylogeny.findTaxidByName(NcbiTaxonomyPhylogeny.java:351)
	at edu.berkeley.compbio.ncbitaxonomy.NcbiTaxonomyPhylogeny.findTaxidByName(NcbiTaxonomyPhylogeny.java:106)
	at edu.berkeley.compbio.phyloutils.PhylogenyTypeConverter.copyValuesToNode(PhylogenyTypeConverter.java:129)
	at edu.berkeley.compbio.phyloutils.PhylogenyTypeConverter.convertToIDTree(PhylogenyTypeConverter.java:48)
	at edu.berkeley.compbio.ncbitaxonomy.NcbiCiccarelliHybridServiceImplTest.ciccarelliTreeIsConvertedToTaxIdTree(NcbiCiccarelliHybridServiceImplTest.java:197)

Standard Output

2012-07-06 17:38:24,739 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Cache key: itol090314_name.tree, false
2012-07-06 17:38:24,781 [main] INFO  com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/testCacheedu.berkeley.compbio.phyloutils.CiccarelliTaxonomyService/itol090314_name.tree, false.basePhylogeny
2012-07-06 17:38:24,782 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Caches not found for itol090314_name.tree, false, reloading...
2012-07-06 17:38:24,796 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 1
2012-07-06 17:38:24,797 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 2
2012-07-06 17:38:24,797 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 3
2012-07-06 17:38:24,798 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 4
2012-07-06 17:38:24,798 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 5
2012-07-06 17:38:24,798 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 6
2012-07-06 17:38:24,799 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 1
2012-07-06 17:38:24,799 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 2
2012-07-06 17:38:24,800 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 3
2012-07-06 17:38:24,800 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 4
2012-07-06 17:38:24,800 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 5
2012-07-06 17:38:24,801 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Staphylococcus subclade not unique, substituting Staphylococcus subclade 1
2012-07-06 17:38:24,801 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacillus subclade not unique, substituting Bacillus subclade 1
2012-07-06 17:38:24,802 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 1
2012-07-06 17:38:24,802 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 2
2012-07-06 17:38:24,802 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 3
2012-07-06 17:38:24,803 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 4
2012-07-06 17:38:24,803 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 5
2012-07-06 17:38:24,803 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 6
2012-07-06 17:38:24,804 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasmataceae subclade not unique, substituting Mycoplasmataceae subclade 1
2012-07-06 17:38:24,804 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 1
2012-07-06 17:38:24,805 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 2
2012-07-06 17:38:24,805 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 3
2012-07-06 17:38:24,805 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 1
2012-07-06 17:38:24,806 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 2
2012-07-06 17:38:24,806 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 3
2012-07-06 17:38:24,806 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Chlamydophila subclade not unique, substituting Chlamydophila subclade 1
2012-07-06 17:38:24,807 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Chlamydophila subclade not unique, substituting Chlamydophila subclade 2
2012-07-06 17:38:24,807 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 4
2012-07-06 17:38:24,807 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 5
2012-07-06 17:38:24,808 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycobacterium subclade not unique, substituting Mycobacterium subclade 1
2012-07-06 17:38:24,808 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycobacterium subclade not unique, substituting Mycobacterium subclade 2
2012-07-06 17:38:24,809 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Corynebacterium subclade not unique, substituting Corynebacterium subclade 1
2012-07-06 17:38:24,809 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 6
2012-07-06 17:38:24,809 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 7
2012-07-06 17:38:24,810 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 8
2012-07-06 17:38:24,810 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 9
2012-07-06 17:38:24,810 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 10
2012-07-06 17:38:24,811 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 11
2012-07-06 17:38:24,811 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 1
2012-07-06 17:38:24,811 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 2
2012-07-06 17:38:24,812 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 3
2012-07-06 17:38:24,812 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 4
2012-07-06 17:38:24,812 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 5
2012-07-06 17:38:24,813 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 12
2012-07-06 17:38:24,813 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 13
2012-07-06 17:38:24,814 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Proteobacteria subclade not unique, substituting Proteobacteria subclade 1
2012-07-06 17:38:24,814 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Rhizobiales subclade not unique, substituting Rhizobiales subclade 1
2012-07-06 17:38:24,814 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Proteobacteria subclade not unique, substituting Proteobacteria subclade 2
2012-07-06 17:38:24,815 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 1
2012-07-06 17:38:24,815 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 2
2012-07-06 17:38:24,816 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 3
2012-07-06 17:38:24,816 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Vibrio subclade not unique, substituting Vibrio subclade 1
2012-07-06 17:38:24,816 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 4
2012-07-06 17:38:24,817 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 1
2012-07-06 17:38:24,817 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 2
2012-07-06 17:38:24,817 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 3
2012-07-06 17:38:24,818 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Escherichia subclade not unique, substituting Escherichia subclade 1
2012-07-06 17:38:24,824 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 4
2012-07-06 17:38:24,824 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 5
2012-07-06 17:38:24,825 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 6
2012-07-06 17:38:24,981 [main] INFO  com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/testCacheedu.berkeley.compbio.ncbitaxonomy.NcbiTaxonomyPhylogeny/ancestorPathCache