You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Hi,
Have run into a NumberFormatException running Ion Torrent VCF files. Neither the supplied test VCF (TSVC_variants.vcf.gz) nor any of my own work, and I get the same error:
$ vtc VS -s I -i TSVC_variants.vcf.gz
2016-05-09 08:27:34 INFO VarStatsEngine:91 - Namespace(SUMMARY=I, OUTPUT=null, pheno=null, VCF=[TSVC_variants.vcf.gz], association=false, DETAILED=null)
2016-05-09 08:27:34 INFO AbstractVariantPool:135 - Opening TSVC_variants.vcf.gz for reading...
2016-05-09 08:27:34 INFO AbstractVariantPool:211 - Setting samples
2016-05-09 08:27:34 ERROR VarStatsEngine:184 - Caught unexpected exception, something is very wrong!
java.lang.NumberFormatException: Infinite or NaN
at java.math.BigDecimal.<init>(BigDecimal.java:895)
at java.math.BigDecimal.<init>(BigDecimal.java:872)
at vtc.tools.utilitybelt.UtilityBelt.round(UtilityBelt.java:57)
at vtc.tools.varstats.VariantPoolSummarizer.getPercents(VariantPoolSummarizer.java:340)
at vtc.tools.varstats.VariantPoolSummarizer.summarizeVariantPool(VariantPoolSummarizer.java:226)
at vtc.tools.varstats.VariantPoolSummarizer.summarizeVariantPools(VariantPoolSummarizer.java:178)
at vtc.tools.varstats.VarStatsEngine.doStats(VarStatsEngine.java:146)
at vtc.VTCEngine.main(VTCEngine.java:66)
The other test VCFs work fine, and so I think this is strictly related to this particular dataset. I did re-install / re-compile the package with unit tests turned on, and all passed except for the VarStatsTest:
Test set: vtc.tools.varstats.VarStatsTest
-------------------------------------------------------------------------------
Tests run: 7, Failures: 3, Errors: 0, Skipped: 0, Time elapsed: 0.035 sec <<< FAILURE! - in vtc.tools.varstats.VarStatsTest
testIndDetailedCombinedSummaryOneFile(vtc.tools.varstats.VarStatsTest) Time elapsed: 0.007 sec <<< FAILURE!
java.lang.AssertionError: null
at org.junit.Assert.fail(Assert.java:86)
at org.junit.Assert.assertTrue(Assert.java:41)
at org.junit.Assert.assertTrue(Assert.java:52)
at vtc.tools.varstats.VarStatsTest.Compare2DetailedSummaryFiles(VarStatsTest.java:438)
at vtc.tools.varstats.VarStatsTest.testIndDetailedCombinedSummaryOneFile(VarStatsTest.java:392)
testCombinedSummary2Files(vtc.tools.varstats.VarStatsTest) Time elapsed: 0.008 sec <<< FAILURE!
java.lang.AssertionError: null
at org.junit.Assert.fail(Assert.java:86)
at org.junit.Assert.assertTrue(Assert.java:41)
at org.junit.Assert.assertTrue(Assert.java:52)
at vtc.tools.varstats.VarStatsTest.Compare2DetailedSummaryFiles(VarStatsTest.java:438)
at vtc.tools.varstats.VarStatsTest.testCombinedSummary2Files(VarStatsTest.java:424)
testIndDetailedSummary(vtc.tools.varstats.VarStatsTest) Time elapsed: 0.012 sec <<< FAILURE!
java.lang.AssertionError: null
at org.junit.Assert.fail(Assert.java:86)
at org.junit.Assert.assertTrue(Assert.java:41)
at org.junit.Assert.assertTrue(Assert.java:52)
at vtc.tools.varstats.VarStatsTest.Compare2DetailedSummaryFiles(VarStatsTest.java:438)
at vtc.tools.varstats.VarStatsTest.testIndDetailedSummary(VarStatsTest.java:361)
So, might be some issue with that particular component? Not sure what other info I can provide, but happy to help where possible.
The text was updated successfully, but these errors were encountered:
Hi,
Have run into a NumberFormatException running Ion Torrent VCF files. Neither the supplied test VCF (TSVC_variants.vcf.gz) nor any of my own work, and I get the same error:
The other test VCFs work fine, and so I think this is strictly related to this particular dataset. I did re-install / re-compile the package with unit tests turned on, and all passed except for the VarStatsTest:
So, might be some issue with that particular component? Not sure what other info I can provide, but happy to help where possible.
The text was updated successfully, but these errors were encountered: