When I run GetBayesianHetCoverage in a Docker container, the function exits without completing with code 247. The Docker container is built from an image that uses the Debian "Stretch" base image, with openjdk version "1.8.0_141" and GATK4.beta.5 added. When I run the same code on my local machine with the same OS, java, and GATK versions, the code runs fine. However, whenever the code is run inside my Docker container, whether locally or on a cloud service, I see this error. Any ideas? Error messages are below.
Traceback (most recent call last):
File "call_het_snps_and_merge_coverage_workflow_launch.py", line 83, in
main()
File "call_het_snps_and_merge_coverage_workflow_launch.py", line 69, in main
gatk_tmp_dir=paths['temp'])
File "/usr/gitc/call_het_snps_and_merge_coverage_workflow.py", line 312, in call_het_snps_and_merge_coverage_workflow
get_het_step()
File "/usr/local/lib/python3.5/dist-packages/plumbum/commands/base.py", line 96, in call
return self.run(args, **kwargs)[1]
File "/usr/local/lib/python3.5/dist-packages/plumbum/commands/base.py", line 226, in run
return p.run()
File "/usr/local/lib/python3.5/dist-packages/plumbum/commands/base.py", line 188, in runner
return run_proc(p, retcode, timeout)
File "/usr/local/lib/python3.5/dist-packages/plumbum/commands/processes.py", line 206, in run_proc
return _check_process(proc, retcode, timeout, stdout, stderr)
File "/usr/local/lib/python3.5/dist-packages/plumbum/commands/processes.py", line 23, in _check_process
proc.verify(retcode, timeout, stdout, stderr)
File "/usr/local/lib/python3.5/dist-packages/plumbum/machines/base.py", line 22, in verify
stdout, stderr)
plumbum.commands.processes.ProcessExecutionError: Command line: ['/usr/gitc/gatk-4.beta.5/gatk-launch', '--javaOptions', '-Xmx32g -Djava.io.tmpdir=/docker_scratch/gSEQWorkflow-b6e4b3ee-d898-4534-92c5-598269d78433/temp', 'GetBayesianHetCoverage', '--reference', '/docker_scratch/reference/Homo_sapiens_assembly38.fasta', '--snpIntervals', '/docker_scratch/reference/1000G.phase1.omni2.5.hapmap3.3.ENTIRE.dbsnp146.PADDEDINTERVALSONLY.interval_list', '--tumor', '/docker_scratch/gSEQWorkflow-b6e4b3ee-d898-4534-92c5-598269d78433/aligned/0_S2_L001_001_170829_M05411_0012_000000000-BDYV8.bam', '--tumorHets', '/docker_scratch/gSEQWorkflow-b6e4b3ee-d898-4534-92c5-598269d78433/het_coverage/0_S2_L001_001_170829_M05411_0012_000000000-BDYV8.het.tsv', '--minimumAbnormalFraction', '0.5', '--maximumAbnormalFraction', '0.8', '--readDepthThreshold', '15', '--quadratureOrder', '200', '--hetCallingStringency', '30.0']
Exit code: 247
Stdout: | 15:00:49.096 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/gitc/gatk-4.beta.5/gatk-package-4.beta.5-local.jar!/com/intel/gkl/native/libgkl_compression.so
| 15:00:49.275 INFO GetBayesianHetCoverage - HTSJDK Defaults.COMPRESSION_LEVEL : 1
| 15:00:49.275 INFO GetBayesianHetCoverage - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
| 15:00:49.275 INFO GetBayesianHetCoverage - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
| 15:00:49.275 INFO GetBayesianHetCoverage - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
| 15:00:49.275 INFO GetBayesianHetCoverage - Deflater: IntelDeflater
| 15:00:49.275 INFO GetBayesianHetCoverage - Inflater: IntelInflater
| 15:00:49.275 INFO GetBayesianHetCoverage - GCS max retries/reopens: 20
| 15:00:49.275 INFO GetBayesianHetCoverage - Using google-cloud-java patch c035098b5e62cb4fe9155eff07ce88449a361f5d from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
| 15:00:49.275 INFO GetBayesianHetCoverage - Initializing engine
| 15:00:49.275 INFO GetBayesianHetCoverage - Done initializing engine
| 15:00:49.275 INFO GetBayesianHetCoverage - TUMOR_ONLY mode selected.
Stderr: | Using GATK jar /usr/gitc/gatk-4.beta.5/gatk-package-4.beta.5-local.jar
| Running:
| java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=1 -Dsnappy.disable=true -Xmx32g -Djava.io.tmpdir=/docker_scratch/gSEQWorkflow-b6e4b3ee-d898-4534-92c5-598269d78433/temp -jar /usr/gitc/gatk-4.beta.5/gatk-package-4.beta.5-local.jar GetBayesianHetCoverage --reference /docker_scratch/reference/Homo_sapiens_assembly38.fasta --snpIntervals /docker_scratch/reference/1000G.phase1.omni2.5.hapmap3.3.ENTIRE.dbsnp146.PADDEDINTERVALSONLY.interval_list --tumor /docker_scratch/gSEQWorkflow-b6e4b3ee-d898-4534-92c5-598269d78433/aligned/0_S2_L001_001_170829_M05411_0012_000000000-BDYV8.bam --tumorHets /docker_scratch/gSEQWorkflow-b6e4b3ee-d898-4534-92c5-598269d78433/het_coverage/0_S2_L001_001_170829_M05411_0012_000000000-BDYV8.het.tsv --minimumAbnormalFraction 0.5 --maximumAbnormalFraction 0.8 --readDepthThreshold 15 --quadratureOrder 200 --hetCallingStringency 30.0
| [September 27, 2017 3:00:49 PM UTC] GetBayesianHetCoverage --reference /docker_scratch/reference/Homo_sapiens_assembly38.fasta --tumor /docker_scratch/gSEQWorkflow-b6e4b3ee-d898-4534-92c5-598269d78433/aligned/0_S2_L001_001_170829_M05411_0012_000000000-BDYV8.bam --snpIntervals /docker_scratch/reference/1000G.phase1.omni2.5.hapmap3.3.ENTIRE.dbsnp146.PADDEDINTERVALSONLY.interval_list --tumorHets /docker_scratch/gSEQWorkflow-b6e4b3ee-d898-4534-92c5-598269d78433/het_coverage/0_S2_L001_001_170829_M05411_0012_000000000-BDYV8.het.tsv --readDepthThreshold 15 --hetCallingStringency 30.0 --minimumAbnormalFraction 0.5 --maximumAbnormalFraction 0.8 --quadratureOrder 200 --minimumMappingQuality 30 --minimumBaseQuality 20 --VALIDATION_STRINGENCY SILENT --maximumCopyNumber 2 --errorAdjustmentFactor 1.0 --help false --version false --showHidden false --verbosity INFO --QUIET false --use_jdk_deflater false --use_jdk_inflater false --gcs_max_retries 20
| [September 27, 2017 3:00:49 PM UTC] Executing as root@7b36c74459e6 on Linux 4.9.41-moby amd64; OpenJDK 64-Bit Server VM 1.8.0_141-8u141-b15-1~deb9u1-b15; Version: 4.beta.5