Failed

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

Failing for the past 8 builds (Since #1 )
Took 1.5 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 20:04:46,185 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Cache key: itol090314_name.tree, false
2012-07-06 20:04:46,330 [main] INFO  com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/testCacheedu.berkeley.compbio.phyloutils.CiccarelliTaxonomyService/itol090314_name.tree, false.basePhylogeny
2012-07-06 20:04:46,331 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Caches not found for itol090314_name.tree, false, reloading...
2012-07-06 20:04:46,514 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 1
2012-07-06 20:04:46,517 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 2
2012-07-06 20:04:46,518 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 3
2012-07-06 20:04:46,518 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 4
2012-07-06 20:04:46,519 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 5
2012-07-06 20:04:46,519 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 6
2012-07-06 20:04:46,529 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 1
2012-07-06 20:04:46,529 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 2
2012-07-06 20:04:46,530 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 3
2012-07-06 20:04:46,530 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 4
2012-07-06 20:04:46,531 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 5
2012-07-06 20:04:46,531 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Staphylococcus subclade not unique, substituting Staphylococcus subclade 1
2012-07-06 20:04:46,535 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacillus subclade not unique, substituting Bacillus subclade 1
2012-07-06 20:04:46,536 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 1
2012-07-06 20:04:46,536 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 2
2012-07-06 20:04:46,537 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 3
2012-07-06 20:04:46,537 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 4
2012-07-06 20:04:46,539 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 5
2012-07-06 20:04:46,541 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 6
2012-07-06 20:04:46,542 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasmataceae subclade not unique, substituting Mycoplasmataceae subclade 1
2012-07-06 20:04:46,542 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 1
2012-07-06 20:04:46,544 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 2
2012-07-06 20:04:46,545 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 3
2012-07-06 20:04:46,546 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 1
2012-07-06 20:04:46,613 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 2
2012-07-06 20:04:46,613 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 3
2012-07-06 20:04:46,614 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Chlamydophila subclade not unique, substituting Chlamydophila subclade 1
2012-07-06 20:04:46,614 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Chlamydophila subclade not unique, substituting Chlamydophila subclade 2
2012-07-06 20:04:46,615 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 4
2012-07-06 20:04:46,615 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 5
2012-07-06 20:04:46,616 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycobacterium subclade not unique, substituting Mycobacterium subclade 1
2012-07-06 20:04:46,616 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycobacterium subclade not unique, substituting Mycobacterium subclade 2
2012-07-06 20:04:46,617 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Corynebacterium subclade not unique, substituting Corynebacterium subclade 1
2012-07-06 20:04:46,620 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 6
2012-07-06 20:04:46,621 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 7
2012-07-06 20:04:46,621 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 8
2012-07-06 20:04:46,622 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 9
2012-07-06 20:04:46,622 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 10
2012-07-06 20:04:46,622 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 11
2012-07-06 20:04:46,624 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 1
2012-07-06 20:04:46,625 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 2
2012-07-06 20:04:46,625 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 3
2012-07-06 20:04:46,625 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 4
2012-07-06 20:04:46,626 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 5
2012-07-06 20:04:46,628 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 12
2012-07-06 20:04:46,629 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 13
2012-07-06 20:04:46,629 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Proteobacteria subclade not unique, substituting Proteobacteria subclade 1
2012-07-06 20:04:46,631 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Rhizobiales subclade not unique, substituting Rhizobiales subclade 1
2012-07-06 20:04:46,632 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Proteobacteria subclade not unique, substituting Proteobacteria subclade 2
2012-07-06 20:04:46,633 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 1
2012-07-06 20:04:46,633 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 2
2012-07-06 20:04:46,633 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 3
2012-07-06 20:04:46,634 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Vibrio subclade not unique, substituting Vibrio subclade 1
2012-07-06 20:04:46,636 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 4
2012-07-06 20:04:46,944 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 1
2012-07-06 20:04:46,944 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 2
2012-07-06 20:04:46,945 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 3
2012-07-06 20:04:46,945 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Escherichia subclade not unique, substituting Escherichia subclade 1
2012-07-06 20:04:46,949 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 4
2012-07-06 20:04:46,949 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 5
2012-07-06 20:04:46,950 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 6
2012-07-06 20:04:47,625 [main] INFO  com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/testCacheedu.berkeley.compbio.ncbitaxonomy.NcbiTaxonomyPhylogeny/ancestorPathCache