Hi,
Here is my log file, what does " java.lang.ClassNotFoundException: org.xerial.snappy.LoadSnappy" mean? Thanks
Using GATK jar /home/kh3/gatk-4.alpha.2-36-g13333ba-SNAPSHOT/gatk-package-4.alpha.2-36-g13333ba-SNAPSHOT-local.jar
Running:
java -jar /home/kh3/gatk-4.alpha.2-36-g13333ba-SNAPSHOT/gatk-package-4.alpha.2-36-g13333ba-SNAPSHOT-local.jar FastqToSam -SM test -F1 /home/kh3/data/Illumina/GATK4/Platinum/Coriell_12891_GCC
AAT_L001_R1_001.fastq.gz -F2 /home/kh3/data/Illumina/GATK4/Platinum/Coriell_12891_GCCAAT_L001_R2_001.fastq.gz -O /home/kh3/data/Illumina/GATK4/Platinum/TEST/test.spark.bam -SO coordinate -R /hom
e/kh3/Resources/genome_b37/genome.2bit --STRIP_UNPAIRED_MATE_NUMBER true --VALIDATION_STRINGENCY LENIENT -PL ILLUMINA --MAX_RECORDS_IN_RAM 6624267
19:28:00.322 INFO IntelGKLUtils - Trying to load Intel GKL library from:
jar:file:/home/kh3/gatk-4.alpha.2-36-g13333ba-SNAPSHOT/gatk-package-4.alpha.2-36-g13333ba-SNAPSHOT-local.jar!/com/intel/gkl/native/libIntelGKL.so
19:28:00.371 INFO IntelGKLUtils - Intel GKL library loaded from classpath.
[September 15, 2016 7:28:00 PM EDT] org.broadinstitute.hellbender.tools.picard.sam.FastqToSam --FASTQ /home/kh3/data/Illumina/GATK4/Platinum/Coriell_12891_GCCAAT_L001_R1_001.fastq.gz --FASTQ2 /home/
kh3/data/Illumina/GATK4/Platinum/Coriell_12891_GCCAAT_L001_R2_001.fastq.gz --output /home/kh3/data/Illumina/GATK4/Platinum/TEST/test.spark.bam --SAMPLE_NAME test --PLATFORM ILLUMINA --SORT_ORDER
coordinate --STRIP_UNPAIRED_MATE_NUMBER true --VALIDATION_STRINGENCY LENIENT --MAX_RECORDS_IN_RAM 6624267 --reference /home/kh3/Resources/genome_b37/genome.2bit --READ_GROUP_NAME A --MIN_Q 0 --MAX_
Q 93 --ALLOW_AND_IGNORE_EMPTY_LINES false --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --verbosity INFO --QUIET false --use_jdk_deflater false
[September 15, 2016 7:28:00 PM EDT] Executing as kh3@rgcaahauva08091.rgc.aws.regeneron.com on Linux 3.13.0-91-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_101-b13; Version: Version:4.alpha.
2-36-g13333ba-SNAPSHOT
19:28:00.397 INFO FastqToSam - Defaults.BUFFER_SIZE : 131072
19:28:00.398 INFO FastqToSam - Defaults.COMPRESSION_LEVEL : 5
19:28:00.398 INFO FastqToSam - Defaults.CREATE_INDEX : false
19:28:00.398 INFO FastqToSam - Defaults.CREATE_MD5 : false
19:28:00.398 INFO FastqToSam - Defaults.CUSTOM_READER_FACTORY :
19:28:00.398 INFO FastqToSam - Defaults.EBI_REFERENCE_SERVICE_URL_MASK : http://www.ebi.ac.uk/ena/cram/md5/%s
19:28:00.398 INFO FastqToSam - Defaults.NON_ZERO_BUFFER_SIZE : 131072
19:28:00.398 INFO FastqToSam - Defaults.REFERENCE_FASTA : null
19:28:00.398 INFO FastqToSam - Defaults.SAM_FLAG_FIELD_FORMAT : DECIMAL
19:28:00.398 INFO FastqToSam - Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
19:28:00.398 INFO FastqToSam - Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : false
19:28:00.398 INFO FastqToSam - Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
19:28:00.398 INFO FastqToSam - Defaults.USE_CRAM_REF_DOWNLOAD : false
19:28:00.398 INFO FastqToSam - Deflater IntelDeflater
19:28:00.398 INFO FastqToSam - Initializing engine
19:28:00.398 INFO FastqToSam - Done initializing engine
19:28:00.489 INFO FastqToSam - Auto-detected quality format as: Standard.
19:28:03.741 INFO FastqToSam - Processed 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: /
19:28:08.820 INFO FastqToSam - Processed 2,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 5s. Last read position: /
19:28:12.281 INFO FastqToSam - Processed 3,000,000 records. Elapsed time: 00:00:11s. Time for last 1,000,000: 3s. Last read position: /
19:28:17.976 INFO FastqToSam - Processed 4,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 5s. Last read position: /
19:28:23.149 INFO FastqToSam - Processed 5,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 5s. Last read position: /
19:28:25.998 INFO FastqToSam - Processed 6,000,000 records. Elapsed time: 00:00:25s. Time for last 1,000,000: 2s. Last read position: /
19:29:16.029 INFO FastqToSam - Shutting down engine
[September 15, 2016 7:29:16 PM EDT] org.broadinstitute.hellbender.tools.picard.sam.FastqToSam done. Elapsed time: 1.26 minutes.
Runtime.totalMemory()=4369416192
Exception in thread "main" java.lang.NoClassDefFoundError: org/xerial/snappy/LoadSnappy
at htsjdk.samtools.util.SnappyLoader.(SnappyLoader.java:86)
at htsjdk.samtools.util.SnappyLoader.(SnappyLoader.java:52)
at htsjdk.samtools.util.TempStreamFactory.getSnappyLoader(TempStreamFactory.java:42)
at htsjdk.samtools.util.TempStreamFactory.wrapTempOutputStream(TempStreamFactory.java:74)
at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:223)
at htsjdk.samtools.util.SortingCollection.add(SortingCollection.java:166)
at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:192)
at org.broadinstitute.hellbender.tools.picard.sam.FastqToSam.doPaired(FastqToSam.java:222)
at org.broadinstitute.hellbender.tools.picard.sam.FastqToSam.makeItSo(FastqToSam.java:181)
at org.broadinstitute.hellbender.tools.picard.sam.FastqToSam.doWork(FastqToSam.java:156)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:109)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:167)
at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram.instanceMain(PicardCommandLineProgram.java:61)
at org.broadinstitute.hellbender.Main.instanceMain(Main.java:76)
at org.broadinstitute.hellbender.Main.main(Main.java:92)
Caused by: java.lang.ClassNotFoundException: org.xerial.snappy.LoadSnappy
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 15 more