UnsatisfiedLinkError when running StructuralVariationDiscoveryPipelineSpark

[jprnz]

Bug Report

When running the StructuralVariationDiscoveryPipelineSpark, I am getting the following error:

java.lang.UnsatisfiedLinkError:`/tmp/jp102/libfml.833188020007107749.jnilib: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /tmp/jp102/libfml.833188020007107749.jnilib)
        at java.lang.ClassLoader$NativeLibrary.load(Native Method)
        at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1941)
        at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1824)
        at java.lang.Runtime.load0(Runtime.java:809)
        at java.lang.System.load(System.java:1086)
        at org.broadinstitute.hellbender.utils.fermi.FermiLiteAssembler.loadNativeLibrary(FermiLiteAssembler.java:157)
        at org.broadinstitute.hellbender.utils.fermi.FermiLiteAssembler.<init>(FermiLiteAssembler.java:24)
        at org.broadinstitute.hellbender.tools.spark.sv.evidence.FermiLiteAssemblyHandler.apply(FermiLiteAssemblyHandler.java:72)
        at org.broadinstitute.hellbender.tools.spark.sv.evidence.FermiLiteAssemblyHandler.apply(FermiLiteAssemblyHandler.java:23)
        at org.apache.spark.api.java.JavaPairRDD$$anonfun$toScalaFunction$1.apply(JavaPairRDD.scala:1040)
        at scala.collection.Iterator$$anon$11.next(Iterator.scala:409)
        at scala.collection.Iterator$class.foreach(Iterator.scala:893)
        at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
        at scala.collection.generic.Growable$class.$plus$plus$eq(Growable.scala:59)
        at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:104)
        at scala.collection.mutable.ArrayBuffer.$plus$plus$eq(ArrayBuffer.scala:48)
        at scala.collection.TraversableOnce$class.to(TraversableOnce.scala:310)
        at scala.collection.AbstractIterator.to(Iterator.scala:1336)
        at scala.collection.TraversableOnce$class.toBuffer(TraversableOnce.scala:302)
        at scala.collection.AbstractIterator.toBuffer(Iterator.scala:1336)
        at scala.collection.TraversableOnce$class.toArray(TraversableOnce.scala:289)
        at scala.collection.AbstractIterator.toArray(Iterator.scala:1336)
        at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:936)
        at org.apache.spark.rdd.RDD$$anonfun$collect$1$$anonfun$13.apply(RDD.scala:936)
        at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2062)
        at org.apache.spark.SparkContext$$anonfun$runJob$5.apply(SparkContext.scala:2062)
        at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
        at org.apache.spark.scheduler.Task.run(Task.scala:108)
        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:335)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
        at java.lang.Thread.run(Thread.java:745)
18/08/29 10:20:49 ERROR Executor: Exception in task 12.0 in stage 12.0 (TID 3228)

I am running version 4.0.8.1 of GATK using openjdk version 1.8.0_212. The command I am using is:

gatk StructuralVariationDiscoveryPipelineSpark \
--aligner-index-image refrance.fasta.img \
--contig-sam-file contigs-aligned.sam \
--spark-master local[30] \
--kmers-to-ignore kmers_to_ignore.txt \
-R $fasta \
-I $sample.bam \
-O $sample.vcf

Thanks for taking a look!

[cwhelan]

@tedsharpe Do you have any thoughts on how to address this?

[tedsharpe]

It appears that the linux version of the packaged libfml was compiled with a different version of gcc than the one on jprnz's machine. (We compile so that we have the right version for a Google dataproc cluster.) I think the best thing to do would be to download git@github.com:broadinstitute/gatk-fermilite-jni.git, and follow the instructions in the last paragraph of the readme for doing a local recompilation.

[jprnz]

@tedsharpe this seems like a reasonable short-term fix.