Failed

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

Failing for the past 11 builds (Since #1 )
Took 2.5 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

2012-07-07 18:39:32,180 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Cache key: itol090314_name.tree, false
2012-07-07 18:39:32,933 [main] INFO  com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/testCacheedu.berkeley.compbio.phyloutils.CiccarelliTaxonomyService/itol090314_name.tree, false.basePhylogeny
2012-07-07 18:39:33,026 [main] INFO  edu.berkeley.compbio.phyloutils.NewickStringTaxonomyService - Caches not found for itol090314_name.tree, false, reloading...
2012-07-07 18:39:33,174 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 1
2012-07-07 18:39:33,175 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 2
2012-07-07 18:39:33,175 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 3
2012-07-07 18:39:33,176 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 4
2012-07-07 18:39:33,180 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 5
2012-07-07 18:39:33,181 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Eukaryota subclade not unique, substituting Eukaryota subclade 6
2012-07-07 18:39:33,181 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 1
2012-07-07 18:39:33,182 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 2
2012-07-07 18:39:33,182 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 3
2012-07-07 18:39:33,190 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 4
2012-07-07 18:39:33,191 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Euryarchaeota subclade not unique, substituting Euryarchaeota subclade 5
2012-07-07 18:39:33,191 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Staphylococcus subclade not unique, substituting Staphylococcus subclade 1
2012-07-07 18:39:33,192 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacillus subclade not unique, substituting Bacillus subclade 1
2012-07-07 18:39:33,192 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 1
2012-07-07 18:39:33,193 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 2
2012-07-07 18:39:33,193 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 3
2012-07-07 18:39:33,193 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 4
2012-07-07 18:39:33,198 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 5
2012-07-07 18:39:33,199 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Streptococcus subclade not unique, substituting Streptococcus subclade 6
2012-07-07 18:39:33,199 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasmataceae subclade not unique, substituting Mycoplasmataceae subclade 1
2012-07-07 18:39:33,200 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 1
2012-07-07 18:39:33,200 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 2
2012-07-07 18:39:33,200 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycoplasma subclade not unique, substituting Mycoplasma subclade 3
2012-07-07 18:39:33,201 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 1
2012-07-07 18:39:33,201 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 2
2012-07-07 18:39:33,267 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 3
2012-07-07 18:39:33,267 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Chlamydophila subclade not unique, substituting Chlamydophila subclade 1
2012-07-07 18:39:33,268 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Chlamydophila subclade not unique, substituting Chlamydophila subclade 2
2012-07-07 18:39:33,268 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 4
2012-07-07 18:39:33,269 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 5
2012-07-07 18:39:33,269 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycobacterium subclade not unique, substituting Mycobacterium subclade 1
2012-07-07 18:39:33,270 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Mycobacterium subclade not unique, substituting Mycobacterium subclade 2
2012-07-07 18:39:33,274 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Corynebacterium subclade not unique, substituting Corynebacterium subclade 1
2012-07-07 18:39:33,274 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 6
2012-07-07 18:39:33,275 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 7
2012-07-07 18:39:33,276 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 8
2012-07-07 18:39:33,276 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 9
2012-07-07 18:39:33,277 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 10
2012-07-07 18:39:33,277 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 11
2012-07-07 18:39:33,278 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 1
2012-07-07 18:39:33,278 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 2
2012-07-07 18:39:33,286 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 3
2012-07-07 18:39:33,287 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 4
2012-07-07 18:39:33,287 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Cyanobacteria subclade not unique, substituting Cyanobacteria subclade 5
2012-07-07 18:39:33,288 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 12
2012-07-07 18:39:33,288 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Bacteria subclade not unique, substituting Bacteria subclade 13
2012-07-07 18:39:33,289 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Proteobacteria subclade not unique, substituting Proteobacteria subclade 1
2012-07-07 18:39:33,289 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Rhizobiales subclade not unique, substituting Rhizobiales subclade 1
2012-07-07 18:39:33,290 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Proteobacteria subclade not unique, substituting Proteobacteria subclade 2
2012-07-07 18:39:33,296 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 1
2012-07-07 18:39:33,297 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 2
2012-07-07 18:39:33,297 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 3
2012-07-07 18:39:33,298 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Vibrio subclade not unique, substituting Vibrio subclade 1
2012-07-07 18:39:33,298 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Gammaproteobacteria subclade not unique, substituting Gammaproteobacteria subclade 4
2012-07-07 18:39:33,299 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 1
2012-07-07 18:39:33,303 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 2
2012-07-07 18:39:33,304 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 3
2012-07-07 18:39:33,304 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Escherichia subclade not unique, substituting Escherichia subclade 1
2012-07-07 18:39:33,312 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 4
2012-07-07 18:39:33,312 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 5
2012-07-07 18:39:33,313 [main] WARN  com.davidsoergel.trees.BasicPhylogenyNode - Name Enterobacteriaceae subclade not unique, substituting Enterobacteriaceae subclade 6
2012-07-07 18:39:34,562 [main] INFO  com.davidsoergel.dsutils.CacheManager - Loading cache: /tmp/testCacheedu.berkeley.compbio.ncbitaxonomy.NcbiTaxonomyPhylogeny/ancestorPathCache