Starting QC
[Time: 2018-06-28 22:18:42] [Mem usage: [84MB / 2024MB]] [Elapsed Time: 00:00:00.0000]
QoRTs is Running in paired-end mode.
QoRTs is Running in name-sorted mode.
NOTE: Function "overlapMatch" requires function "mismatchEngine". Adding "mismatchEngine" to the active function list...
Running functions: CigarOpDistribution, GCDistribution, GeneCalcs, InsertSize, 
        JunctionCalcs, NVC, QualityScoreDistribution, StrandCheck, 
        chromCounts, cigarLocusCounts, mismatchEngine, overlapMatch, 
        readLengthDistro, writeBiotypeCounts, writeClippedNVC, 
        writeDESeq, writeDEXSeq, writeGeneBody, writeGeneCounts, 
        writeGenewiseGeneBody, writeJunctionSeqCounts, 
        writeKnownSplices, writeNovelSplices, writeSpliceExon
Checking first 10000 reads. Checking SAM file for formatting errors...
[bam_sort_core] merging from 10 files...
Exception in thread "main" java.lang.NoClassDefFoundError: net/sf/samtools/util/BlockGunzipper
	at net.sf.samtools.util.BlockCompressedInputStream.<init>(BlockCompressedInputStream.java:60)
	at net.sf.samtools.util.BlockCompressedInputStream.<init>(BlockCompressedInputStream.java:67)
	at net.sf.samtools.SAMFileReader.isBAMFile(SAMFileReader.java:690)
	at net.sf.samtools.SAMFileReader.init(SAMFileReader.java:640)
	at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:161)
	at net.sf.samtools.SAMFileReader.<init>(SAMFileReader.java:131)
	at qcUtils.runAllQC$.runOnSeqFile(runAllQC.scala:1010)
	at qcUtils.runAllQC$.run(runAllQC.scala:960)
	at qcUtils.runAllQC$allQC_runner.run(runAllQC.scala:672)
	at runner.runner$.main(runner.scala:97)
	at runner.runner.main(runner.scala)
Caused by: java.lang.ClassNotFoundException: net.sf.samtools.util.BlockGunzipper
	at java.net.URLClassLoader$1.run(URLClassLoader.java:370)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 11 more
Caused by: java.util.zip.ZipException: error reading zip file
	at java.util.zip.ZipFile.read(Native Method)
	at java.util.zip.ZipFile.access$1400(ZipFile.java:60)
	at java.util.zip.ZipFile$ZipFileInputStream.read(ZipFile.java:734)
	at java.util.zip.ZipFile$ZipFileInflaterInputStream.fill(ZipFile.java:434)
	at java.util.zip.InflaterInputStream.read(InflaterInputStream.java:158)
	at sun.misc.Resource.getBytes(Resource.java:124)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:462)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
	... 17 more