Dear GATK developers, I am running the following command to perform SV calling with StructuralVariationDiscoveryPipelineSpark:
nohup /home/simone/software/gatk-4.0.3.0/gatk --java-options -Xmx100G StructuralVariationDiscoveryPipelineSpark \
-I /home/simone/Project_Nebbiolo/10x_Genomics/n423_SVs_validation_alignment/outs/n423.bam \
-R Neb71.PB.Primary.plus.Haplotigs_merged.2bit \
--contig-sam-file n423_SVs_GATK_SV_contigs.sam \
--aligner-index-image Neb71.PB.Primary.plus.Haplotigs_merged.fasta.img \
--kmers-to-ignore BadKmers.out \
-O n423_GATK_SVs.vcf &
and i keep getting these ERROR messages:
19/05/27 08:12:34 ERROR TaskSchedulerImpl: Lost executor driver on localhost: Executor heartbeat timed out after 143709 ms
19/05/27 16:41:48 ERROR Executor: Exception in task 15.0 in stage 8.0 (TID 7111)
19/05/27 16:41:48 ERROR SparkUncaughtExceptionHandler: Uncaught exception in thread Thread[Executor task launch worker for task 7102,5,main]
19/05/27 16:54:19 ERROR Executor: Exception in task 31.0 in stage 8.0 (TID 7127)
19/05/27 16:41:48 ERROR SparkUncaughtExceptionHandler: Uncaught exception in thread Thread[Executor task launch worker for task 7099,5,main]
19/05/27 17:46:42 ERROR Executor: Exception in task 26.0 in stage 8.0 (TID 7122)
19/05/27 19:05:49 ERROR SparkUncaughtExceptionHandler: [Container in shutdown] Uncaught exception in thread Thread[Executor task launch worker for task 7121,5,main]
19/05/27 18:46:10 ERROR Executor: Exception in task 20.0 in stage 8.0 (TID 7116)
19/05/27 19:34:32 ERROR SparkUncaughtExceptionHandler: [Container in shutdown] Uncaught exception in thread Thread[Executor task launch worker for task 7108,5,main]
19/05/27 19:48:22 ERROR Executor: Exception in task 32.0 in stage 8.0 (TID 7128)
19/05/27 19:48:22 ERROR SparkUncaughtExceptionHandler: [Container in shutdown] Uncaught exception in thread Thread[Executor task launch worker for task 7128,5,main]
19/05/27 20:10:58 ERROR Executor: Exception in task 33.0 in stage 8.0 (TID 7129)
19/05/27 20:10:58 ERROR SparkUncaughtExceptionHandler: [Container in shutdown] Uncaught exception in thread Thread[Executor task launch worker for task 7129,5,main]
19/05/27 20:10:58 ERROR TaskSetManager: Task 7 in stage 8.0 failed 1 times; aborting job
19/05/27 20:11:08 ERROR ShutdownHookManager: ShutdownHookManger shutdown forcefully.
19/05/27 20:11:08 ERROR Utils: Uncaught exception in thread pool-7-thread-1
I would really appreciate any help you could provide on how to solve these issues.
Thank you in advanced.
Luciano
nohup /home/simone/software/gatk-4.0.3.0/gatk --java-options -Xmx100G StructuralVariationDiscoveryPipelineSpark \
-I /home/simone/Project_Nebbiolo/10x_Genomics/n423_SVs_validation_alignment/outs/n423.bam \
-R Neb71.PB.Primary.plus.Haplotigs_merged.2bit \
--contig-sam-file n423_SVs_GATK_SV_contigs.sam \
--aligner-index-image Neb71.PB.Primary.plus.Haplotigs_merged.fasta.img \
--kmers-to-ignore BadKmers.out \
-O n423_GATK_SVs.vcf &
and i keep getting these ERROR messages:
19/05/27 08:12:34 ERROR TaskSchedulerImpl: Lost executor driver on localhost: Executor heartbeat timed out after 143709 ms
19/05/27 16:41:48 ERROR Executor: Exception in task 15.0 in stage 8.0 (TID 7111)
19/05/27 16:41:48 ERROR SparkUncaughtExceptionHandler: Uncaught exception in thread Thread[Executor task launch worker for task 7102,5,main]
19/05/27 16:54:19 ERROR Executor: Exception in task 31.0 in stage 8.0 (TID 7127)
19/05/27 16:41:48 ERROR SparkUncaughtExceptionHandler: Uncaught exception in thread Thread[Executor task launch worker for task 7099,5,main]
19/05/27 17:46:42 ERROR Executor: Exception in task 26.0 in stage 8.0 (TID 7122)
19/05/27 19:05:49 ERROR SparkUncaughtExceptionHandler: [Container in shutdown] Uncaught exception in thread Thread[Executor task launch worker for task 7121,5,main]
19/05/27 18:46:10 ERROR Executor: Exception in task 20.0 in stage 8.0 (TID 7116)
19/05/27 19:34:32 ERROR SparkUncaughtExceptionHandler: [Container in shutdown] Uncaught exception in thread Thread[Executor task launch worker for task 7108,5,main]
19/05/27 19:48:22 ERROR Executor: Exception in task 32.0 in stage 8.0 (TID 7128)
19/05/27 19:48:22 ERROR SparkUncaughtExceptionHandler: [Container in shutdown] Uncaught exception in thread Thread[Executor task launch worker for task 7128,5,main]
19/05/27 20:10:58 ERROR Executor: Exception in task 33.0 in stage 8.0 (TID 7129)
19/05/27 20:10:58 ERROR SparkUncaughtExceptionHandler: [Container in shutdown] Uncaught exception in thread Thread[Executor task launch worker for task 7129,5,main]
19/05/27 20:10:58 ERROR TaskSetManager: Task 7 in stage 8.0 failed 1 times; aborting job
19/05/27 20:11:08 ERROR ShutdownHookManager: ShutdownHookManger shutdown forcefully.
19/05/27 20:11:08 ERROR Utils: Uncaught exception in thread pool-7-thread-1
I would really appreciate any help you could provide on how to solve these issues.
Thank you in advanced.
Luciano