recalibrate=true fails, Unsupported class file major version 55

[asalimih]

Version info

• bcbio version: 1.2.9
• OS name and version: Ubuntu 18.04.5 LTS

To Reproduce
Exact bcbio command you have used:

bcbio_nextgen.py ../config/config.yaml -n 8

Your yaml configuration file:

details:
- algorithm:
    aligner: bwa
    exclude_regions: [lcr]
    mark_duplicates: true
    recalibrate: true
    variantcaller: [mutect2, strelka2, varscan, vardict]
    variant_regions: /media/gpudrive/apps/bcbio/genomes/Hsapiens/GRCh37/coverage/capture_regions/Exome-NGv3.bed
  analysis: variant2
  description: Patient70-normal
  files:
    - normal_1.fq.gz
    - normal_2.fq.gz
  genome_build: GRCh37
  metadata:
    batch: Patient70
    phenotype: normal
- algorithm:
    aligner: bwa
    mark_duplicates: true
    recalibrate: true
    remove_lcr: true
    variantcaller: [mutect2, strelka2, varscan, vardict]
    variant_regions: /media/gpudrive/apps/bcbio/genomes/Hsapiens/GRCh37/coverage/capture_regions/Exome-NGv3.bed
  analysis: variant2
  description: Patient70-tumor
  files:
    - tumor_1.fq.gz
    - tumor_2.fq.gz
  genome_build: GRCh37
  metadata:
    batch: Patient70
    phenotype: tumor
upload:
    dir: ../final

Log files (could be found in work/log)
Here are the important parts of the log I guess

[2022-12-25T18:24Z] GATK: BaseRecalibratorSpark
[2022-12-25T18:25Z] 18:25:59.390 INFO  BaseRecalibratorSpark - ------------------------------------------------------------
[2022-12-25T18:25Z] 18:25:59.391 INFO  BaseRecalibratorSpark - The Genome Analysis Toolkit (GATK) v4.2.6.1
[2022-12-25T18:25Z] 18:25:59.391 INFO  BaseRecalibratorSpark - For support and documentation go to https://software.broadinstitute.org/gatk/
[2022-12-25T18:25Z] 18:25:59.391 INFO  BaseRecalibratorSpark - Executing as asalimi@gpu on Linux v4.15.0-197-generic amd64
[2022-12-25T18:25Z] 18:25:59.391 INFO  BaseRecalibratorSpark - Java runtime: OpenJDK 64-Bit Server VM v11.0.9.1-internal+0-adhoc..src
[2022-12-25T18:25Z] 18:25:59.392 INFO  BaseRecalibratorSpark - Start Date/Time: December 25, 2022 at 6:25:03 PM UTC
[2022-12-25T18:25Z] 18:25:59.392 INFO  BaseRecalibratorSpark - ------------------------------------------------------------
[2022-12-25T18:25Z] 18:25:59.392 INFO  BaseRecalibratorSpark - ------------------------------------------------------------
[2022-12-25T18:25Z] 18:25:59.393 INFO  BaseRecalibratorSpark - HTSJDK Version: 2.24.1
[2022-12-25T18:25Z] 18:25:59.393 INFO  BaseRecalibratorSpark - Picard Version: 2.27.1
[2022-12-25T18:25Z] 18:25:59.393 INFO  BaseRecalibratorSpark - Built for Spark Version: 2.4.5

...
[2022-12-25T18:36Z] java.lang.IllegalArgumentException: Unsupported class file major version 55
[2022-12-25T18:36Z]     at org.apache.xbean.asm6.ClassReader.<init>(ClassReader.java:166)
[2022-12-25T18:36Z]     at org.apache.xbean.asm6.ClassReader.<init>(ClassReader.java:148)
[2022-12-25T18:36Z]     at org.apache.xbean.asm6.ClassReader.<init>(ClassReader.java:136)
[2022-12-25T18:36Z]     at org.apache.xbean.asm6.ClassReader.<init>(ClassReader.java:237)
[2022-12-25T18:36Z]     at org.apache.spark.util.ClosureCleaner$.getClassReader(ClosureCleaner.scala:49)
[2022-12-25T18:36Z]     at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:517)
[2022-12-25T18:36Z]     at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:500)
[2022-12-25T18:36Z]     at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:733)
[2022-12-25T18:36Z]     at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:134)
[2022-12-25T18:36Z]     at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:134)
[2022-12-25T18:36Z]     at scala.collection.mutable.HashTable$class.foreachEntry(HashTable.scala:236)
[2022-12-25T18:36Z]     at scala.collection.mutable.HashMap.foreachEntry(HashMap.scala:40)
[2022-12-25T18:36Z]     at scala.collection.mutable.HashMap$$anon$1.foreach(HashMap.scala:134)
[2022-12-25T18:36Z]     at scala.collection.TraversableLike$WithFilter.foreach(TraversableLike.scala:732)
[2022-12-25T18:36Z]     at org.apache.spark.util.FieldAccessFinder$$anon$3.visitMethodInsn(ClosureCleaner.scala:500)
[2022-12-25T18:36Z]     at org.apache.xbean.asm6.ClassReader.readCode(ClassReader.java:2175)
[2022-12-25T18:36Z]     at org.apache.xbean.asm6.ClassReader.readMethod(ClassReader.java:1238)
[2022-12-25T18:36Z]     at org.apache.xbean.asm6.ClassReader.accept(ClassReader.java:631)
[2022-12-25T18:36Z]     at org.apache.xbean.asm6.ClassReader.accept(ClassReader.java:355)
[2022-12-25T18:36Z]     at org.apache.spark.util.ClosureCleaner$$anonfun$org$apache$spark$util$ClosureCleaner$$clean$14.apply(ClosureCleaner.scala:307)
[2022-12-25T18:36Z]     at org.apache.spark.util.ClosureCleaner$$anonfun$org$apache$spark$util$ClosureCleaner$$clean$14.apply(ClosureCleaner.scala:306)
[2022-12-25T18:36Z]     at scala.collection.immutable.List.foreach(List.scala:392)
[2022-12-25T18:36Z]     at org.apache.spark.util.ClosureCleaner$.org$apache$spark$util$ClosureCleaner$$clean(ClosureCleaner.scala:306)
[2022-12-25T18:36Z]     at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:162)
[2022-12-25T18:36Z]     at org.apache.spark.SparkContext.clean(SparkContext.scala:2326)
[2022-12-25T18:36Z]     at org.apache.spark.SparkContext.runJob(SparkContext.scala:2100)
[2022-12-25T18:36Z]     at org.apache.spark.SparkContext.runJob(SparkContext.scala:2126)
[2022-12-25T18:36Z]     at org.apache.spark.rdd.RDD$$anonfun$collect$1.apply(RDD.scala:990)
[2022-12-25T18:36Z]     at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
[2022-12-25T18:36Z]     at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
[2022-12-25T18:36Z]     at org.apache.spark.rdd.RDD.withScope(RDD.scala:385)
[2022-12-25T18:36Z]     at org.apache.spark.rdd.RDD.collect(RDD.scala:989)
[2022-12-25T18:36Z]     at org.apache.spark.RangePartitioner$.sketch(Partitioner.scala:309)
[2022-12-25T18:36Z]     at org.apache.spark.RangePartitioner.<init>(Partitioner.scala:171)
[2022-12-25T18:36Z]     at org.apache.spark.RangePartitioner.<init>(Partitioner.scala:151)
[2022-12-25T18:36Z]     at org.apache.spark.rdd.OrderedRDDFunctions$$anonfun$sortByKey$1.apply(OrderedRDDFunctions.scala:62)
[2022-12-25T18:36Z]     at org.apache.spark.rdd.OrderedRDDFunctions$$anonfun$sortByKey$1.apply(OrderedRDDFunctions.scala:61)
[2022-12-25T18:36Z]     at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
[2022-12-25T18:36Z]     at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
[2022-12-25T18:36Z]     at org.apache.spark.rdd.RDD.withScope(RDD.scala:385)
[2022-12-25T18:36Z]     at org.apache.spark.rdd.OrderedRDDFunctions.sortByKey(OrderedRDDFunctions.scala:61)
[2022-12-25T18:36Z]     at org.apache.spark.api.java.JavaPairRDD.sortByKey(JavaPairRDD.scala:936)
[2022-12-25T18:36Z]     at org.broadinstitute.hellbender.utils.spark.SparkUtils.sortUsingElementsAsKeys(SparkUtils.java:165)
[2022-12-25T18:36Z]     at org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink.sortSamRecordsToMatchHeader(ReadsSparkSink.java:207)
[2022-12-25T18:36Z]     at org.broadinstitute.hellbender.engine.spark.datasources.ReadsSparkSink.writeReads(ReadsSparkSink.java:107)
[2022-12-25T18:36Z]     at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.writeReads(GATKSparkTool.java:374)
[2022-12-25T18:36Z]     at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.writeReads(GATKSparkTool.java:362)
[2022-12-25T18:36Z]     at org.broadinstitute.hellbender.tools.spark.ApplyBQSRSpark.runTool(ApplyBQSRSpark.java:90)
[2022-12-25T18:36Z]     at org.broadinstitute.hellbender.engine.spark.GATKSparkTool.runPipeline(GATKSparkTool.java:546)
[2022-12-25T18:36Z]     at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:31)
[2022-12-25T18:36Z]     at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
[2022-12-25T18:36Z]     at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
[2022-12-25T18:36Z]     at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
[2022-12-25T18:36Z]     at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
[2022-12-25T18:36Z]     at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
[2022-12-25T18:36Z]     at org.broadinstitute.hellbender.Main.main(Main.java:289)
[2022-12-25T18:36Z] 22/12/25 18:36:31 INFO ShutdownHookManager: Shutdown hook called
Using GATK jar /pathto/bcbio/anaconda/envs/java/share/gatk4-4.2.6.1-1/gatk-package-4.2.6.1-local.jar

[naumenko-sa]

Hi @asalimih !

It think it is a java-related error. Could you please check which java is being used to run gatk in your env?
I has to be pathto/bcbio/anaconda/envs/java/bin/java

SN

[asalimih]

Hi @asalimih !

It think it is a java-related error. Could you please check which java is being used to run gatk in your env? I has to be pathto/bcbio/anaconda/envs/java/bin/java

SN

Hi, Thanks for your reply,
It seems it uses the correct java:

$ which java
/media/gpudrive/apps/bcbio/anaconda/bin/java
$ /media/gpudrive/apps/bcbio/anaconda/bin/java --version
openjdk 11.0.9.1-internal 2020-11-04
OpenJDK Runtime Environment (build 11.0.9.1-internal+0-adhoc..src)
OpenJDK 64-Bit Server VM (build 11.0.9.1-internal+0-adhoc..src, mixed mode)

[tsuyoi]

Hi @asalimih !
It think it is a java-related error. Could you please check which java is being used to run gatk in your env? I has to be pathto/bcbio/anaconda/envs/java/bin/java
SN

Hi, Thanks for your reply, It seems it uses the correct java:

$ which java
/media/gpudrive/apps/bcbio/anaconda/bin/java
$ /media/gpudrive/apps/bcbio/anaconda/bin/java --version
openjdk 11.0.9.1-internal 2020-11-04
OpenJDK Runtime Environment (build 11.0.9.1-internal+0-adhoc..src)
OpenJDK 64-Bit Server VM (build 11.0.9.1-internal+0-adhoc..src, mixed mode)

@naumenko-sa ,

I am seeing this same error and in reading this it seems different versions of java exist in different paths.

On my install (bcbio 1.2.9), there is the {bcbio}/anaconda/bin/java:

$:{bcbio}/anaconda/bin$ ./java -version
openjdk version "11.0.9.1-internal" 2020-11-04
OpenJDK Runtime Environment (build 11.0.9.1-internal+0-adhoc..src)
OpenJDK 64-Bit Server VM (build 11.0.9.1-internal+0-adhoc..src, mixed mode)

and {bcbio}/anaconda/envs/java/bin/java:

$:{bcbio}/anaconda/envs/java/bin$ ./java -version
openjdk version "1.8.0_332"
OpenJDK Runtime Environment (Zulu 8.62.0.19-CA-linux64) (build 1.8.0_332-b09)
OpenJDK 64-Bit Server VM (Zulu 8.62.0.19-CA-linux64) (build 25.332-b09, mixed mode)

These are both separate from my $PATH java (if it matters):

$ which java
/usr/bin/java
$ java -version
openjdk version "11.0.16" 2022-07-19
OpenJDK Runtime Environment (build 11.0.16+8-post-Ubuntu-0ubuntu120.04)
OpenJDK 64-Bit Server VM (build 11.0.16+8-post-Ubuntu-0ubuntu120.04, mixed mode, sharing)

I'm new to bcbio_nextgen so hopefully I'm looking in the right place(s).