created by AmandaChamberlain
on 2017-05-25
I’ve used Picard2.1 MarkDuplicates for a bunch of bam files (4-40x coverage) generated with Picard2.1 MergeSamFiles and it works fine. I’m trying to get GATK4-Alpha MarkDuplicates working on the bam files generated with GATK4-Alpha MergeSamFiles and it works fine for my lower coverage samples (4-5x) but anything greater than 8x is crashing. I get the following output
```
[May 24, 2017 7:43:27 PM AEST] org.broadinstitute.hellbender.tools.picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 98.36 minutes.
Runtime.totalMemory()=64997556224
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 org.broadinstitute.hellbender.tools.picard.sam.markduplicates.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:246) at org.broadinstitute.hellbender.tools.picard.sam.markduplicates.MarkDuplicates.doWork(MarkDuplicates.java:83) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:102) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:155) at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram.instanceMain(PicardCommandLineProgram.java:61) at org.broadinstitute.hellbender.Main.instanceMain(Main.java:69) at org.broadinstitute.hellbender.Main.main(Main.java:84)
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) … 13 more
```
Can you provide any guidance on what is causing it to crash?
From AmandaChamberlain on 2017-05-25
I should add that I used command
```
java -Xmx80G -jar $GATK MarkDuplicates -I ${SAMPLE}.sorted.bam -O ${SAMPLE}_dedup.bam -M ${SAMPLE}_dedup.metrics —CREATE_INDEX true —VALIDATION_STRINGENCY LENIENT —OPTICAL_DUPLICATE_PIXEL_DISTANCE 100
```
From sd21 on 2017-05-30
Hi Amanda,
I think I have had aa similar error relating to snappy. You can turn it off by using “-Dsnappy.disable=true” after your java command.
Hope that helps,
Steve
From Sheila on 2017-05-31
AmandaChamberlain sd21
Hi,
Steve is correct that this can happen when you run GATK4 without the gatk-launch script. gatk-launch sets an important system property: -Dsnappy.disable=true
You should run GATK4 via gatk-launch, as the README suggests.
-Sheila