Downloading 's3://seqr-dp-conf--prod/bin/spark-submit-hail' to '/mnt/var/lib/hadoop/steps/s-JHS5PJSM8YLK/.' Could not find valid SPARK_HOME while searching ['/mnt/var/lib/hadoop/steps', '/usr/local/bin'] SLF4J: Class path contains multiple SLF4J bindings. SLF4J: Found binding in [jar:file:/usr/lib/spark/jars/slf4j-log4j12-1.7.16.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: Found binding in [jar:file:/usr/share/aws/emr/emrfs/lib/slf4j-log4j12-1.7.12.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation. SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory] Using properties file: /usr/lib/spark/conf/spark-defaults.conf Adding default property: spark.sql.warehouse.dir=hdfs:///user/spark/warehouse Adding default property: spark.sql.parquet.fs.optimized.committer.optimization-enabled=true Adding default property: spark.history.fs.logDirectory=hdfs:///var/log/spark/apps Adding default property: spark.hadoop.mapreduce.fileoutputcommitter.algorithm.version.emr_internal_use_only.EmrFileSystem=2 Adding default property: spark.hadoop.mapreduce.output.fs.optimized.committer.enabled=true Adding default property: spark.eventLog.enabled=true Adding default property: spark.shuffle.service.enabled=true Adding default property: spark.driver.extraLibraryPath=/usr/lib/hadoop/lib/native:/usr/lib/hadoop-lzo/lib/native Adding default property: spark.emr.default.executor.memory=349207M Adding default property: spark.yarn.historyServer.address=ip-172-23-93-109.ec2.internal:18080 Adding default property: spark.stage.attempt.ignoreOnDecommissionFetchFailure=true Adding default property: spark.driver.memory=11171M Adding default property: spark.executor.instances=4 Adding default property: spark.emr.maximizeResourceAllocation=true Adding default property: spark.files.fetchFailure.unRegisterOutputOnHost=true Adding default property: spark.default.parallelism=384 Adding default property: spark.executor.defaultJavaOptions=-verbose:gc -XX:+PrintGCDetails -XX:+PrintGCDateStamps -XX:OnOutOfMemoryError='kill -9 %p' Adding default property: spark.resourceManager.cleanupExpiredHost=true Adding default property: spark.fileMetadataCache.enabled=false Adding default property: spark.yarn.appMasterEnv.SPARK_PUBLIC_DNS=$(hostname -f) Adding default property: spark.sql.emr.internal.extensions=com.amazonaws.emr.spark.EmrSparkSessionExtensions Adding default property: spark.emr.default.executor.cores=48 Adding default property: spark.hadoop.fs.s3.getObject.initialSocketTimeoutMilliseconds=2000 Adding default property: spark.master=yarn Adding default property: spark.sql.parquet.output.committer.class=com.amazon.emr.committer.EmrOptimizedSparkSqlParquetOutputCommitter Adding default property: spark.driver.defaultJavaOptions=-XX:OnOutOfMemoryError='kill -9 %p' Adding default property: spark.blacklist.decommissioning.timeout=1h Adding default property: spark.executor.extraLibraryPath=/usr/lib/hadoop/lib/native:/usr/lib/hadoop-lzo/lib/native Adding default property: spark.sql.hive.metastore.sharedPrefixes=com.amazonaws.services.dynamodbv2 Adding default property: spark.executor.memory=349207M Adding default property: spark.driver.extraClassPath=/usr/lib/hadoop-lzo/lib/*:/usr/lib/hadoop/hadoop-aws.jar:/usr/share/aws/aws-java-sdk/*:/usr/share/aws/emr/goodies/lib/emr-spark-goodies.jar:/usr/share/aws/emr/security/conf:/usr/share/aws/emr/security/lib/*:/usr/share/aws/hmclient/lib/aws-glue-datacatalog-spark-client.jar:/usr/share/java/Hive-JSON-Serde/hive-openx-serde.jar:/usr/share/aws/sagemaker-spark-sdk/lib/sagemaker-spark-sdk.jar:/usr/share/aws/emr/s3select/lib/emr-s3-select-spark-connector.jar Adding default property: spark.eventLog.dir=hdfs:///var/log/spark/apps Adding default property: spark.dynamicAllocation.enabled=true Adding default property: spark.executor.extraClassPath=/usr/lib/hadoop-lzo/lib/*:/usr/lib/hadoop/hadoop-aws.jar:/usr/share/aws/aws-java-sdk/*:/usr/share/aws/emr/goodies/lib/emr-spark-goodies.jar:/usr/share/aws/emr/security/conf:/usr/share/aws/emr/security/lib/*:/usr/share/aws/hmclient/lib/aws-glue-datacatalog-spark-client.jar:/usr/share/java/Hive-JSON-Serde/hive-openx-serde.jar:/usr/share/aws/sagemaker-spark-sdk/lib/sagemaker-spark-sdk.jar:/usr/share/aws/emr/s3select/lib/emr-s3-select-spark-connector.jar Adding default property: spark.executor.cores=48 Adding default property: spark.history.ui.port=18080 Adding default property: spark.emr.default.executor.instances=4 Adding default property: spark.blacklist.decommissioning.enabled=true Adding default property: spark.decommissioning.timeout.threshold=20 Adding default property: spark.hadoop.mapreduce.fileoutputcommitter.cleanup-failures.ignored.emr_internal_use_only.EmrFileSystem=true Adding default property: spark.hadoop.yarn.timeline-service.enabled=false Parsed arguments: master yarn deployMode null executorMemory 349207M executorCores 48 totalExecutorCores null propertiesFile /usr/lib/spark/conf/spark-defaults.conf driverMemory 11171M driverCores null driverExtraClassPath /home/hadoop/hail-0.2.57-spark-2.4.8.jar:/usr/share/aws/emr/emrfs/lib/emrfs-hadoop-assembly-2.48.0.jar:/home/hadoop/commons-httpclient-3.1.jar driverExtraLibraryPath /usr/lib/hadoop/lib/native:/usr/lib/hadoop-lzo/lib/native driverExtraJavaOptions null supervise false queue null numExecutors 4 files null pyFiles null archives null mainClass null primaryResource file:/home/hadoop/hail-elasticsearch-pipelines/luigi_pipeline/seqr_loading.py name seqr_loading.py childArgs [SeqrMTToESTask] jars file:/home/hadoop/hail-0.2.57-spark-2.4.8.jar packages null packagesExclusions null repositories null verbose true Spark properties used, including those specified through --conf and those from the properties file /usr/lib/spark/conf/spark-defaults.conf: (spark.sql.emr.internal.extensions,com.amazonaws.emr.spark.EmrSparkSessionExtensions) (spark.executor.defaultJavaOptions,-verbose:gc -XX:+PrintGCDetails -XX:+PrintGCDateStamps -XX:OnOutOfMemoryError='kill -9 %p') (spark.blacklist.decommissioning.timeout,1h) (spark.emr.default.executor.instances,4) (spark.emr.maximizeResourceAllocation,true) (spark.blacklist.decommissioning.enabled,true) (spark.executor.extraLibraryPath,/usr/lib/hadoop/lib/native:/usr/lib/hadoop-lzo/lib/native) (spark.default.parallelism,384) (spark.hadoop.yarn.timeline-service.enabled,false) (spark.fileMetadataCache.enabled,false) (spark.driver.memory,11171M) (spark.network.timeout,600) (spark.executor.memory,349207M) (spark.executor.instances,4) (spark.driver.extraLibraryPath,/usr/lib/hadoop/lib/native:/usr/lib/hadoop-lzo/lib/native) (spark.sql.parquet.fs.optimized.committer.optimization-enabled,true) (spark.sql.warehouse.dir,hdfs:///user/spark/warehouse) (spark.yarn.historyServer.address,ip-172-23-93-109.ec2.internal:18080) (spark.rpc.message.maxSize,512) (spark.eventLog.enabled,true) (spark.files.fetchFailure.unRegisterOutputOnHost,true) (spark.hadoop.fs.s3.getObject.initialSocketTimeoutMilliseconds,2000) (spark.stage.attempt.ignoreOnDecommissionFetchFailure,true) (spark.history.ui.port,18080) (spark.yarn.appMasterEnv.SPARK_PUBLIC_DNS,$(hostname -f)) (spark.driver.defaultJavaOptions,-XX:OnOutOfMemoryError='kill -9 %p') (spark.resourceManager.cleanupExpiredHost,true) (spark.history.fs.logDirectory,hdfs:///var/log/spark/apps) (spark.shuffle.service.enabled,true) (spark.emr.default.executor.cores,48) (spark.hadoop.mapreduce.fileoutputcommitter.algorithm.version.emr_internal_use_only.EmrFileSystem,2) (spark.executor.heartbeatInterval,30s) (spark.jars,/home/hadoop/hail-0.2.57-spark-2.4.8.jar) (spark.task.maxFailures,10) (spark.hadoop.mapreduce.output.fs.optimized.committer.enabled,true) (spark.executor.extraClassPath,hail-0.2.57-spark-2.4.8.jar:/usr/share/aws/emr/emrfs/lib/emrfs-hadoop-assembly-2.48.0.jar:/home/hadoop/commons-httpclient-3.1.jar) (spark.sql.hive.metastore.sharedPrefixes,com.amazonaws.services.dynamodbv2) (spark.eventLog.dir,hdfs:///var/log/spark/apps) (spark.master,yarn) (spark.emr.default.executor.memory,349207M) (spark.dynamicAllocation.enabled,true) (spark.sql.parquet.output.committer.class,com.amazon.emr.committer.EmrOptimizedSparkSqlParquetOutputCommitter) (spark.executor.cores,48) (spark.decommissioning.timeout.threshold,20) (spark.hadoop.mapreduce.fileoutputcommitter.cleanup-failures.ignored.emr_internal_use_only.EmrFileSystem,true) (spark.driver.extraClassPath,/home/hadoop/hail-0.2.57-spark-2.4.8.jar:/usr/share/aws/emr/emrfs/lib/emrfs-hadoop-assembly-2.48.0.jar:/home/hadoop/commons-httpclient-3.1.jar) Main class: org.apache.spark.deploy.PythonRunner Arguments: file:/home/hadoop/hail-elasticsearch-pipelines/luigi_pipeline/seqr_loading.py null SeqrMTToESTask Spark config: (spark.sql.warehouse.dir,hdfs:///user/spark/warehouse) (spark.sql.parquet.fs.optimized.committer.optimization-enabled,true) (spark.history.fs.logDirectory,hdfs:///var/log/spark/apps) (spark.hadoop.mapreduce.fileoutputcommitter.algorithm.version.emr_internal_use_only.EmrFileSystem,2) (spark.hadoop.mapreduce.output.fs.optimized.committer.enabled,true) (spark.eventLog.enabled,true) (spark.executor.heartbeatInterval,30s) (spark.shuffle.service.enabled,true) (spark.driver.extraLibraryPath,/usr/lib/hadoop/lib/native:/usr/lib/hadoop-lzo/lib/native) (spark.emr.default.executor.memory,349207M) (spark.jars,file:/home/hadoop/hail-0.2.57-spark-2.4.8.jar) (spark.yarn.historyServer.address,ip-172-23-93-109.ec2.internal:18080) (spark.stage.attempt.ignoreOnDecommissionFetchFailure,true) (spark.app.name,seqr_loading.py) (spark.network.timeout,600) (spark.driver.memory,11171M) (spark.executor.instances,4) (spark.emr.maximizeResourceAllocation,true) (spark.files.fetchFailure.unRegisterOutputOnHost,true) (spark.default.parallelism,384) (spark.executor.defaultJavaOptions,-verbose:gc -XX:+PrintGCDetails -XX:+PrintGCDateStamps -XX:OnOutOfMemoryError='kill -9 %p') (spark.resourceManager.cleanupExpiredHost,true) (spark.fileMetadataCache.enabled,false) (spark.yarn.appMasterEnv.SPARK_PUBLIC_DNS,$(hostname -f)) (spark.sql.emr.internal.extensions,com.amazonaws.emr.spark.EmrSparkSessionExtensions) (spark.emr.default.executor.cores,48) (spark.hadoop.fs.s3.getObject.initialSocketTimeoutMilliseconds,2000) (spark.submit.deployMode,client) (spark.master,yarn) (spark.sql.parquet.output.committer.class,com.amazon.emr.committer.EmrOptimizedSparkSqlParquetOutputCommitter) (spark.rpc.message.maxSize,512) (spark.driver.defaultJavaOptions,-XX:OnOutOfMemoryError='kill -9 %p') (spark.blacklist.decommissioning.timeout,1h) (spark.executor.extraLibraryPath,/usr/lib/hadoop/lib/native:/usr/lib/hadoop-lzo/lib/native) (spark.sql.hive.metastore.sharedPrefixes,com.amazonaws.services.dynamodbv2) (spark.executor.memory,349207M) (spark.driver.extraClassPath,/home/hadoop/hail-0.2.57-spark-2.4.8.jar:/usr/share/aws/emr/emrfs/lib/emrfs-hadoop-assembly-2.48.0.jar:/home/hadoop/commons-httpclient-3.1.jar) (spark.eventLog.dir,hdfs:///var/log/spark/apps) (spark.dynamicAllocation.enabled,true) (spark.executor.extraClassPath,hail-0.2.57-spark-2.4.8.jar:/usr/share/aws/emr/emrfs/lib/emrfs-hadoop-assembly-2.48.0.jar:/home/hadoop/commons-httpclient-3.1.jar) (spark.executor.cores,48) (spark.history.ui.port,18080) (spark.repl.local.jars,file:///home/hadoop/hail-0.2.57-spark-2.4.8.jar) (spark.yarn.isPython,true) (spark.emr.default.executor.instances,4) (spark.blacklist.decommissioning.enabled,true) (spark.decommissioning.timeout.threshold,20) (spark.hadoop.mapreduce.fileoutputcommitter.cleanup-failures.ignored.emr_internal_use_only.EmrFileSystem,true) (spark.yarn.dist.jars,file:///home/hadoop/hail-0.2.57-spark-2.4.8.jar) (spark.hadoop.yarn.timeline-service.enabled,false) (spark.task.maxFailures,10) Classpath elements: file:///home/hadoop/hail-0.2.57-spark-2.4.8.jar WARNING:luigi-interface:Loading GCP module without the python packages httplib2, google-auth. This *could* crash at runtime if no other credentials are provided. WARNING:luigi-interface:Loading GCS module without the python packages googleapiclient & google-auth. This will crash at runtime if GCS functionality is used. INFO:root:Index name: iuis_panelv1_20220321__wgs__grch38__variants__20220531 accessing remote ES: https://search-seqr-gris-prod-65wdlm6cncfxo5d326vkd4z6be.us-east-1.es.amazonaws.com:443 current AWS identity identifier: arn:aws:sts::353534673745:assumed-role/emr-ec2-instance-role/i-0be9ea5d6c0092374 INFO:elasticsearch:GET https://search-seqr-gris-prod-65wdlm6cncfxo5d326vkd4z6be.us-east-1.es.amazonaws.com:443/ [status:200 request:0.051s] INFO:root:{'cluster_name': '353534673745:seqr-gris-prod', 'cluster_uuid': 'bxEo9Xo7QASXzS9Uog285Q', 'name': 'kFwTrBC', 'tagline': 'You Know, for Search', 'version': {'build_date': '2021-11-03T19:01:02.985059Z', 'build_flavor': 'oss', 'build_hash': 'f27534d', 'build_snapshot': False, 'build_type': 'zip', 'lucene_version': '7.7.0', 'minimum_index_compatibility_version': '5.0.0', 'minimum_wire_compatibility_version': '5.6.0', 'number': '6.8.0'}} INFO:luigi:logging configured by default settings DEBUG: Checking if SeqrMTToESTask(source_path=s3://seqr-dp-build--prod/mt-hail-luigi/emr-test/IUIS_PANELv1_20220321.mt, use_temp_loading_nodes=True, project_guid=IUIS_PANELv1_20220321, sample_type=WGS, genome_version=38, dataset_type=VARIANTS, family_id=, individual_id=, es_host=https://search-seqr-gris-prod-65wdlm6cncfxo5d326vkd4z6be.us-east-1.es.amazonaws.com, es_port=443, es_index=, num_shards=25, dest_file=s3://seqr-dp-build--prod/mt-hail-luigi/emr-test/IUIS_PANELv1_20220321_SUCCESS_TO_ES) is complete DEBUG:luigi-interface:Checking if SeqrMTToESTask(source_path=s3://seqr-dp-build--prod/mt-hail-luigi/emr-test/IUIS_PANELv1_20220321.mt, use_temp_loading_nodes=True, project_guid=IUIS_PANELv1_20220321, sample_type=WGS, genome_version=38, dataset_type=VARIANTS, family_id=, individual_id=, es_host=https://search-seqr-gris-prod-65wdlm6cncfxo5d326vkd4z6be.us-east-1.es.amazonaws.com, es_port=443, es_index=, num_shards=25, dest_file=s3://seqr-dp-build--prod/mt-hail-luigi/emr-test/IUIS_PANELv1_20220321_SUCCESS_TO_ES) is complete DEBUG: no credentials provided, delegating credentials resolution to boto3 DEBUG:luigi-interface:no credentials provided, delegating credentials resolution to boto3 DEBUG: Path s3://seqr-dp-build--prod/mt-hail-luigi/emr-test/IUIS_PANELv1_20220321_SUCCESS_TO_ES does not exist DEBUG:luigi-interface:Path s3://seqr-dp-build--prod/mt-hail-luigi/emr-test/IUIS_PANELv1_20220321_SUCCESS_TO_ES does not exist DEBUG: Checking if SeqrVCFToMTTask(source_paths=["s3://seqr-dp-data--prod/vcf/prod/IUIS_PANELv1_20220321.vcf.gz"], dest_path=s3://seqr-dp-build--prod/mt-hail-luigi/emr-test/IUIS_PANELv1_20220321.mt, genome_version=38, array_elements_required=False, vep_runner=VEP, reference_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/all_reference_data/combined_reference_data_grch38.ht, clinvar_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/CLINVAR/clinvar.GRCh38.2022-04-12.ht, hgmd_like_csv_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/HGMD_LIKE/GRCh38_HGMD_LIKE_2022_01_Seqr2.csv, hgmd_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/HGMD/hgmd_2022.1_hg38.ht, cidr_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/CIDR.ht, nisc_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/NISC.ht, bgi_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/BGI.ht, hgsc_wes_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/HGSC_WES.ht, hgsc_wgs_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/HGSC_WGS_101_130.ht, sample_type=WGS, validate=False, dataset_type=VARIANTS, remap_path=, subset_path=) is complete DEBUG:luigi-interface:Checking if SeqrVCFToMTTask(source_paths=["s3://seqr-dp-data--prod/vcf/prod/IUIS_PANELv1_20220321.vcf.gz"], dest_path=s3://seqr-dp-build--prod/mt-hail-luigi/emr-test/IUIS_PANELv1_20220321.mt, genome_version=38, array_elements_required=False, vep_runner=VEP, reference_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/all_reference_data/combined_reference_data_grch38.ht, clinvar_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/CLINVAR/clinvar.GRCh38.2022-04-12.ht, hgmd_like_csv_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/HGMD_LIKE/GRCh38_HGMD_LIKE_2022_01_Seqr2.csv, hgmd_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/HGMD/hgmd_2022.1_hg38.ht, cidr_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/CIDR.ht, nisc_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/NISC.ht, bgi_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/BGI.ht, hgsc_wes_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/HGSC_WES.ht, hgsc_wgs_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/HGSC_WGS_101_130.ht, sample_type=WGS, validate=False, dataset_type=VARIANTS, remap_path=, subset_path=) is complete DEBUG: no credentials provided, delegating credentials resolution to boto3 DEBUG:luigi-interface:no credentials provided, delegating credentials resolution to boto3 DEBUG: Path s3://seqr-dp-build--prod/mt-hail-luigi/emr-test/IUIS_PANELv1_20220321.mt/_SUCCESS does not exist DEBUG:luigi-interface:Path s3://seqr-dp-build--prod/mt-hail-luigi/emr-test/IUIS_PANELv1_20220321.mt/_SUCCESS does not exist INFO: Informed scheduler that task SeqrMTToESTask_VARIANTS_s3___seqr_dp_bui_https___search_s_2cf222ce9a has status PENDING INFO:luigi-interface:Informed scheduler that task SeqrMTToESTask_VARIANTS_s3___seqr_dp_bui_https___search_s_2cf222ce9a has status PENDING DEBUG: Checking if VcfFile(filename=s3://seqr-dp-data--prod/vcf/prod/IUIS_PANELv1_20220321.vcf.gz) is complete DEBUG:luigi-interface:Checking if VcfFile(filename=s3://seqr-dp-data--prod/vcf/prod/IUIS_PANELv1_20220321.vcf.gz) is complete DEBUG: no credentials provided, delegating credentials resolution to boto3 DEBUG:luigi-interface:no credentials provided, delegating credentials resolution to boto3 INFO: Informed scheduler that task SeqrVCFToMTTask_False_s3___seqr_dp_dat_s3___seqr_dp_dat_9e17b233f4 has status PENDING INFO:luigi-interface:Informed scheduler that task SeqrVCFToMTTask_False_s3___seqr_dp_dat_s3___seqr_dp_dat_9e17b233f4 has status PENDING INFO: Informed scheduler that task VcfFile_s3___seqr_dp_dat_f06b18d9e5 has status DONE INFO:luigi-interface:Informed scheduler that task VcfFile_s3___seqr_dp_dat_f06b18d9e5 has status DONE INFO: Done scheduling tasks INFO:luigi-interface:Done scheduling tasks INFO: Running Worker with 1 processes INFO:luigi-interface:Running Worker with 1 processes DEBUG: Asking scheduler for work... DEBUG:luigi-interface:Asking scheduler for work... DEBUG: Pending tasks: 2 DEBUG:luigi-interface:Pending tasks: 2 INFO: [pid 13023] Worker Worker(salt=198992999, workers=1, host=ip-172-23-93-109, username=hadoop, pid=13023) running SeqrVCFToMTTask(source_paths=["s3://seqr-dp-data--prod/vcf/prod/IUIS_PANELv1_20220321.vcf.gz"], dest_path=s3://seqr-dp-build--prod/mt-hail-luigi/emr-test/IUIS_PANELv1_20220321.mt, genome_version=38, array_elements_required=False, vep_runner=VEP, reference_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/all_reference_data/combined_reference_data_grch38.ht, clinvar_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/CLINVAR/clinvar.GRCh38.2022-04-12.ht, hgmd_like_csv_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/HGMD_LIKE/GRCh38_HGMD_LIKE_2022_01_Seqr2.csv, hgmd_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/HGMD/hgmd_2022.1_hg38.ht, cidr_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/CIDR.ht, nisc_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/NISC.ht, bgi_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/BGI.ht, hgsc_wes_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/HGSC_WES.ht, hgsc_wgs_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/HGSC_WGS_101_130.ht, sample_type=WGS, validate=False, dataset_type=VARIANTS, remap_path=, subset_path=) INFO:luigi-interface:[pid 13023] Worker Worker(salt=198992999, workers=1, host=ip-172-23-93-109, username=hadoop, pid=13023) running SeqrVCFToMTTask(source_paths=["s3://seqr-dp-data--prod/vcf/prod/IUIS_PANELv1_20220321.vcf.gz"], dest_path=s3://seqr-dp-build--prod/mt-hail-luigi/emr-test/IUIS_PANELv1_20220321.mt, genome_version=38, array_elements_required=False, vep_runner=VEP, reference_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/all_reference_data/combined_reference_data_grch38.ht, clinvar_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/CLINVAR/clinvar.GRCh38.2022-04-12.ht, hgmd_like_csv_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/HGMD_LIKE/GRCh38_HGMD_LIKE_2022_01_Seqr2.csv, hgmd_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/HGMD/hgmd_2022.1_hg38.ht, cidr_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/CIDR.ht, nisc_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/NISC.ht, bgi_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/BGI.ht, hgsc_wes_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/HGSC_WES.ht, hgsc_wgs_ht_path=s3://seqr-dp-data--prod/seqr-reference-data/GRCh38/HGSC_WGS_101_130.ht, sample_type=WGS, validate=False, dataset_type=VARIANTS, remap_path=, subset_path=) DEBUG: no credentials provided, delegating credentials resolution to boto3 DEBUG:luigi-interface:no credentials provided, delegating credentials resolution to boto3 Warning (import_vcf in HailMatrixTableTask): using array_elements_required set to False,performance significantly affected! Initializing Hail with default parameters... 2022-05-31 16:34:38 WARN Hail:37 - This Hail JAR was compiled for Spark 2.4.8, running with Spark 2.4.8-amzn-0. Compatibility is not guaranteed. 2022-05-31 16:34:38 INFO SparkContext:54 - Running Spark version 2.4.8-amzn-0 2022-05-31 16:34:38 INFO SparkContext:54 - Submitted application: Hail 2022-05-31 16:34:38 INFO SparkContext:54 - Spark configuration: spark.app.name=Hail spark.blacklist.decommissioning.enabled=true spark.blacklist.decommissioning.timeout=1h spark.decommissioning.timeout.threshold=20 spark.default.parallelism=384 spark.driver.defaultJavaOptions=-XX:OnOutOfMemoryError='kill -9 %p' spark.driver.extraClassPath=/home/hadoop/hail-0.2.57-spark-2.4.8.jar:/usr/share/aws/emr/emrfs/lib/emrfs-hadoop-assembly-2.48.0.jar:/home/hadoop/commons-httpclient-3.1.jar spark.driver.extraLibraryPath=/usr/lib/hadoop/lib/native:/usr/lib/hadoop-lzo/lib/native spark.driver.maxResultSize=0 spark.driver.memory=11171M spark.dynamicAllocation.enabled=true spark.emr.default.executor.cores=48 spark.emr.default.executor.instances=4 spark.emr.default.executor.memory=349207M spark.emr.maximizeResourceAllocation=true spark.eventLog.dir=hdfs:///var/log/spark/apps spark.eventLog.enabled=true spark.executor.cores=48 spark.executor.defaultJavaOptions=-verbose:gc -XX:+PrintGCDetails -XX:+PrintGCDateStamps -XX:OnOutOfMemoryError='kill -9 %p' spark.executor.extraClassPath=hail-0.2.57-spark-2.4.8.jar:/usr/share/aws/emr/emrfs/lib/emrfs-hadoop-assembly-2.48.0.jar:/home/hadoop/commons-httpclient-3.1.jar spark.executor.extraLibraryPath=/usr/lib/hadoop/lib/native:/usr/lib/hadoop-lzo/lib/native spark.executor.heartbeatInterval=30s spark.executor.instances=4 spark.executor.memory=349207M spark.fileMetadataCache.enabled=false spark.files.fetchFailure.unRegisterOutputOnHost=true spark.hadoop.fs.s3.getObject.initialSocketTimeoutMilliseconds=2000 spark.hadoop.io.compression.codecs=org.apache.hadoop.io.compress.DefaultCodec,is.hail.io.compress.BGzipCodec,is.hail.io.compress.BGzipCodecTbi,org.apache.hadoop.io.compress.GzipCodec spark.hadoop.mapreduce.fileoutputcommitter.algorithm.version.emr_internal_use_only.EmrFileSystem=2 spark.hadoop.mapreduce.fileoutputcommitter.cleanup-failures.ignored.emr_internal_use_only.EmrFileSystem=true spark.hadoop.mapreduce.input.fileinputformat.split.minsize=0 spark.hadoop.mapreduce.output.fs.optimized.committer.enabled=true spark.hadoop.yarn.timeline-service.enabled=false spark.history.fs.logDirectory=hdfs:///var/log/spark/apps spark.history.ui.port=18080 spark.jars=file:/home/hadoop/hail-0.2.57-spark-2.4.8.jar spark.kryo.registrator=is.hail.kryo.HailKryoRegistrator spark.kryoserializer.buffer.max=1g spark.logConf=true spark.master=yarn spark.network.timeout=600 spark.repl.local.jars=file:///home/hadoop/hail-0.2.57-spark-2.4.8.jar spark.resourceManager.cleanupExpiredHost=true spark.rpc.message.maxSize=512 spark.serializer=org.apache.spark.serializer.KryoSerializer spark.shuffle.service.enabled=true spark.sql.emr.internal.extensions=com.amazonaws.emr.spark.EmrSparkSessionExtensions spark.sql.hive.metastore.sharedPrefixes=com.amazonaws.services.dynamodbv2 spark.sql.parquet.fs.optimized.committer.optimization-enabled=true spark.sql.parquet.output.committer.class=com.amazon.emr.committer.EmrOptimizedSparkSqlParquetOutputCommitter spark.sql.warehouse.dir=hdfs:///user/spark/warehouse spark.stage.attempt.ignoreOnDecommissionFetchFailure=true spark.submit.deployMode=client spark.task.maxFailures=10 spark.ui.showConsoleProgress=false spark.yarn.appMasterEnv.SPARK_PUBLIC_DNS=$(hostname -f) spark.yarn.dist.jars=file:///home/hadoop/hail-0.2.57-spark-2.4.8.jar spark.yarn.historyServer.address=ip-172-23-93-109.ec2.internal:18080 spark.yarn.isPython=true 2022-05-31 16:34:38 INFO SecurityManager:54 - Changing view acls to: hadoop 2022-05-31 16:34:38 INFO SecurityManager:54 - Changing modify acls to: hadoop 2022-05-31 16:34:38 INFO SecurityManager:54 - Changing view acls groups to: 2022-05-31 16:34:38 INFO SecurityManager:54 - Changing modify acls groups to: 2022-05-31 16:34:38 INFO SecurityManager:54 - SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(hadoop); groups with view permissions: Set(); users with modify permissions: Set(hadoop); groups with modify permissions: Set() 2022-05-31 16:34:39 INFO Utils:54 - Successfully started service 'sparkDriver' on port 45625. 2022-05-31 16:34:39 INFO SparkEnv:54 - Registering MapOutputTracker 2022-05-31 16:34:39 INFO SparkEnv:54 - Registering BlockManagerMaster 2022-05-31 16:34:39 INFO BlockManagerMasterEndpoint:54 - Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information 2022-05-31 16:34:39 INFO BlockManagerMasterEndpoint:54 - BlockManagerMasterEndpoint up 2022-05-31 16:34:39 INFO DiskBlockManager:54 - Created local directory at /mnt/tmp/blockmgr-2f17fd5d-1dba-4f67-b65f-264cb424761f 2022-05-31 16:34:39 INFO MemoryStore:54 - MemoryStore started with capacity 5.6 GB 2022-05-31 16:34:39 INFO SparkEnv:54 - Registering OutputCommitCoordinator 2022-05-31 16:34:39 INFO log:169 - Logging initialized @4983ms to org.spark_project.jetty.util.log.Slf4jLog 2022-05-31 16:34:39 INFO Server:375 - jetty-9.4.z-SNAPSHOT; built: unknown; git: unknown; jvm 1.8.0_332-b08 2022-05-31 16:34:39 INFO Server:415 - Started @5125ms 2022-05-31 16:34:39 INFO AbstractConnector:331 - Started ServerConnector@6a9027b9{HTTP/1.1, (http/1.1)}{0.0.0.0:4040} 2022-05-31 16:34:39 INFO Utils:54 - Successfully started service 'SparkUI' on port 4040. 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@4166c6c3{/jobs,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@11dbe053{/jobs/json,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@63c061b{/jobs/job,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@54db7d59{/jobs/job/json,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@1accd6e9{/stages,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@7c261775{/stages/json,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@3bc83424{/stages/stage,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@4206f9c{/stages/stage/json,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@7e331228{/stages/pool,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@7ff9e960{/stages/pool/json,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@3de831d3{/storage,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@3ab3f57d{/storage/json,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@5cf71251{/storage/rdd,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@6cf54246{/storage/rdd/json,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@106f90a2{/environment,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@355297cf{/environment/json,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@51d36eae{/executors,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@1772e1a0{/executors/json,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@7bf4996c{/executors/threadDump,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@5ab98532{/executors/threadDump/json,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@105536d5{/static,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@2e44cb4{/,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@1050c9f8{/api,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@618e4701{/jobs/job/kill,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@7d3c1c9{/stages/stage/kill,null,AVAILABLE,@Spark} 2022-05-31 16:34:39 INFO SparkUI:54 - Bound SparkUI to 0.0.0.0, and started at http://ip-172-23-93-109.ec2.internal:4040 2022-05-31 16:34:39 INFO SparkContext:54 - Added JAR file:/home/hadoop/hail-0.2.57-spark-2.4.8.jar at spark://ip-172-23-93-109.ec2.internal:45625/jars/hail-0.2.57-spark-2.4.8.jar with timestamp 1654014879683 2022-05-31 16:34:39 INFO Utils:54 - Using 5 preallocated executors (minExecutors: 0). Set spark.dynamicAllocation.preallocateExecutors to `false` disable executor preallocation. 2022-05-31 16:34:40 INFO RMProxy:133 - Connecting to ResourceManager at ip-172-23-93-109.ec2.internal/172.23.93.109:8032 2022-05-31 16:34:40 INFO Client:54 - Requesting a new application from cluster with 4 NodeManagers 2022-05-31 16:34:40 INFO Configuration:2585 - resource-types.xml not found 2022-05-31 16:34:40 INFO ResourceUtils:421 - Unable to find 'resource-types.xml'. 2022-05-31 16:34:40 INFO ResourceUtils:126 - Adding resource type - name = memory-mb, units = Mi, type = COUNTABLE 2022-05-31 16:34:40 INFO ResourceUtils:135 - Adding resource type - name = vcores, units = , type = COUNTABLE 2022-05-31 16:34:40 INFO Client:54 - Verifying our application has not requested more than the maximum memory capability of the cluster (385024 MB per container) 2022-05-31 16:34:40 INFO Client:54 - Will allocate AM container, with 896 MB memory including 384 MB overhead 2022-05-31 16:34:40 INFO Client:54 - Setting up container launch context for our AM 2022-05-31 16:34:40 INFO Client:54 - Setting up the launch environment for our AM container 2022-05-31 16:34:40 INFO Client:54 - Preparing resources for our AM container 2022-05-31 16:34:40 WARN Client:66 - Neither spark.yarn.jars nor spark.yarn.archive is set, falling back to uploading libraries under SPARK_HOME. 2022-05-31 16:34:42 INFO Client:54 - Uploading resource file:/mnt/tmp/spark-f00cca14-2403-4c43-bfaf-c7d07a8ff6ff/__spark_libs__531588892698493859.zip -> hdfs://ip-172-23-93-109.ec2.internal:8020/user/hadoop/.sparkStaging/application_1654014794385_0001/__spark_libs__531588892698493859.zip 2022-05-31 16:34:43 INFO Client:54 - Uploading resource file:/home/hadoop/hail-0.2.57-spark-2.4.8.jar -> hdfs://ip-172-23-93-109.ec2.internal:8020/user/hadoop/.sparkStaging/application_1654014794385_0001/hail-0.2.57-spark-2.4.8.jar 2022-05-31 16:34:43 INFO Client:54 - Uploading resource file:/usr/lib/spark/python/lib/pyspark.zip -> hdfs://ip-172-23-93-109.ec2.internal:8020/user/hadoop/.sparkStaging/application_1654014794385_0001/pyspark.zip 2022-05-31 16:34:44 INFO Client:54 - Uploading resource file:/usr/lib/spark/python/lib/py4j-0.10.7-src.zip -> hdfs://ip-172-23-93-109.ec2.internal:8020/user/hadoop/.sparkStaging/application_1654014794385_0001/py4j-0.10.7-src.zip 2022-05-31 16:34:44 INFO Client:54 - Uploading resource file:/mnt/tmp/spark-f00cca14-2403-4c43-bfaf-c7d07a8ff6ff/__spark_conf__8374655523858296184.zip -> hdfs://ip-172-23-93-109.ec2.internal:8020/user/hadoop/.sparkStaging/application_1654014794385_0001/__spark_conf__.zip 2022-05-31 16:34:44 INFO SecurityManager:54 - Changing view acls to: hadoop 2022-05-31 16:34:44 INFO SecurityManager:54 - Changing modify acls to: hadoop 2022-05-31 16:34:44 INFO SecurityManager:54 - Changing view acls groups to: 2022-05-31 16:34:44 INFO SecurityManager:54 - Changing modify acls groups to: 2022-05-31 16:34:44 INFO SecurityManager:54 - SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(hadoop); groups with view permissions: Set(); users with modify permissions: Set(hadoop); groups with modify permissions: Set() 2022-05-31 16:34:45 INFO Client:54 - Submitting application application_1654014794385_0001 to ResourceManager 2022-05-31 16:34:46 INFO YarnClientImpl:303 - Submitted application application_1654014794385_0001 2022-05-31 16:34:46 INFO SchedulerExtensionServices:54 - Starting Yarn extension services with app application_1654014794385_0001 and attemptId None 2022-05-31 16:34:47 INFO Client:54 - Application report for application_1654014794385_0001 (state: ACCEPTED) 2022-05-31 16:34:47 INFO Client:54 - client token: N/A diagnostics: AM container is launched, waiting for AM container to Register with RM ApplicationMaster host: N/A ApplicationMaster RPC port: -1 queue: default start time: 1654014885985 final status: UNDEFINED tracking URL: http://ip-172-23-93-109.ec2.internal:20888/proxy/application_1654014794385_0001/ user: hadoop 2022-05-31 16:34:48 INFO Client:54 - Application report for application_1654014794385_0001 (state: ACCEPTED) 2022-05-31 16:34:49 INFO Client:54 - Application report for application_1654014794385_0001 (state: ACCEPTED) 2022-05-31 16:34:50 INFO YarnClientSchedulerBackend:54 - Add WebUI Filter. org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter, Map(PROXY_HOSTS -> ip-172-23-93-109.ec2.internal, PROXY_URI_BASES -> http://ip-172-23-93-109.ec2.internal:20888/proxy/application_1654014794385_0001), /proxy/application_1654014794385_0001 2022-05-31 16:34:50 INFO Client:54 - Application report for application_1654014794385_0001 (state: RUNNING) 2022-05-31 16:34:50 INFO Client:54 - client token: N/A diagnostics: N/A ApplicationMaster host: 172.23.92.43 ApplicationMaster RPC port: -1 queue: default start time: 1654014885985 final status: UNDEFINED tracking URL: http://ip-172-23-93-109.ec2.internal:20888/proxy/application_1654014794385_0001/ user: hadoop 2022-05-31 16:34:50 INFO YarnClientSchedulerBackend:54 - Application application_1654014794385_0001 has started running. 2022-05-31 16:34:50 INFO Utils:54 - Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 43507. 2022-05-31 16:34:50 INFO NettyBlockTransferService:54 - Server created on ip-172-23-93-109.ec2.internal:43507 2022-05-31 16:34:50 INFO BlockManager:54 - Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy 2022-05-31 16:34:50 INFO YarnSchedulerBackend$YarnSchedulerEndpoint:54 - ApplicationMaster registered as NettyRpcEndpointRef(spark-client://YarnAM) 2022-05-31 16:34:50 INFO BlockManagerMaster:54 - Registering BlockManager BlockManagerId(driver, ip-172-23-93-109.ec2.internal, 43507, None) 2022-05-31 16:34:50 INFO BlockManagerMasterEndpoint:54 - Registering block manager ip-172-23-93-109.ec2.internal:43507 with 5.6 GB RAM, BlockManagerId(driver, ip-172-23-93-109.ec2.internal, 43507, None) 2022-05-31 16:34:50 INFO BlockManagerMaster:54 - Registered BlockManager BlockManagerId(driver, ip-172-23-93-109.ec2.internal, 43507, None) 2022-05-31 16:34:50 INFO BlockManager:54 - external shuffle service port = 7337 2022-05-31 16:34:50 INFO BlockManager:54 - Initialized BlockManager: BlockManagerId(driver, ip-172-23-93-109.ec2.internal, 43507, None) 2022-05-31 16:34:50 INFO JettyUtils:54 - Adding filter org.apache.hadoop.yarn.server.webproxy.amfilter.AmIpFilter to /metrics/json. 2022-05-31 16:34:50 INFO ContextHandler:916 - Started o.s.j.s.ServletContextHandler@78a711d{/metrics/json,null,AVAILABLE,@Spark} 2022-05-31 16:34:50 INFO SingleEventLogFileWriter:54 - Logging events to hdfs:/var/log/spark/apps/application_1654014794385_0001.inprogress 2022-05-31 16:34:50 INFO Utils:54 - Using 5 preallocated executors (minExecutors: 0). Set spark.dynamicAllocation.preallocateExecutors to `false` disable executor preallocation. 2022-05-31 16:34:50 INFO YarnClientSchedulerBackend:54 - SchedulerBackend is ready for scheduling beginning after reached minRegisteredResourcesRatio: 0.0 2022-05-31 16:34:50 INFO Hail:22 - SparkUI: http://ip-172-23-93-109.ec2.internal:4040 Running on Apache Spark version 2.4.8-amzn-0 SparkUI available at http://ip-172-23-93-109.ec2.internal:4040 Welcome to __ __ <>__ / /_/ /__ __/ / / __ / _ `/ / / /_/ /_/\_,_/_/_/ version 0.2.57-582b2e31b8bd LOGGING: writing to /mnt/var/lib/hadoop/steps/s-JHS5PJSM8YLK/hail-20220531-1634-0.2.57-582b2e31b8bd.log JObject(List((name,JString(VEP)), (config,JString(s3://seqr-dp-data--prod/vep/vep105/vep105-loftee-grch38-aws.json)), (csq,JBool(false)), (blockSize,JInt(1000)))) [Stage 0:> (0 + 192) / 1000] [Stage 0:===> (63 + 192) / 1000] [Stage 0:========> (172 + 192) / 1000] [Stage 0:==============> (274 + 193) / 1000] [Stage 0:=======================> (448 + 192) / 1000] [Stage 0:==============================> (589 + 195) / 1000] [Stage 0:=======================================> (755 + 192) / 1000]2022-05-31 16:34:59 Hail: INFO: Coerced almost-sorted dataset INFO:root:==> Done with VEP WARNING:luigi_pipeline.lib.model.base_mt_schema:MT using schema class already has vep annotation. WARNING:luigi_pipeline.lib.model.base_mt_schema:MT using schema class already has filters annotation. INFO:luigi_pipeline.lib.model.base_mt_schema:Overwriting matrix table annotation filters WARNING:luigi_pipeline.lib.model.base_mt_schema:MT using schema class already has rsid annotation. INFO:luigi_pipeline.lib.model.base_mt_schema:Overwriting matrix table annotation rsid WARNING:luigi_pipeline.lib.model.base_mt_schema:MT using schema class already has vep annotation. INFO:luigi_pipeline.lib.model.base_mt_schema:Overwriting matrix table annotation vep ---------------------------------------- Global fields: 'gencodeVersion': str 'sourceFilePath': str 'genomeVersion': str 'sampleType': str 'hail_version': str ---------------------------------------- Column fields: 's': str ---------------------------------------- Row fields: 'locus': locus 'alleles': array 'aIndex': int32 'AC': int32 'AF': float64 'alt': str 'AN': int32 'cadd': struct { PHRED: float32 } 'clinvar': struct { allele_id: int32, clinical_significance: str, gold_stars: int32 } 'codingGeneIds': set 'contig': str 'dbnsfp': struct { SIFT_pred: str, Polyphen2_HVAR_pred: str, MutationTaster_pred: str, FATHMM_pred: str, MetaSVM_pred: str, REVEL_score: str, GERP_RS: str, phastCons100way_vertebrate: str } 'docId': str 'domains': set 'eigen': struct { Eigen_phred: float64 } 'end': int32 'exac': struct { AF_POPMAX: float64, AF: float64, AC_Adj: int32, AC_Het: int32, AC_Hom: int32, AC_Hemi: int32, AN_Adj: int32 } 'filters': set 'g1k': struct { AC: int32, AF: float64, AN: int32, POPMAX_AF: float64 } 'geneIds': set 'geno2mp': struct { HPO_Count: int32 } 'genotypes': array 'gnomad_exome_coverage': float64 'gnomad_exomes': struct { AF: float64, AN: int32, AC: int32, Hom: int32, AF_POPMAX_OR_GLOBAL: float64, FAF_AF: float64, Hemi: int32 } 'gnomad_genome_coverage': float32 'gnomad_genomes': struct { AF: float64, AN: int32, AC: int32, Hom: int32, AF_POPMAX_OR_GLOBAL: float64, FAF_AF: float64, Hemi: int32 } 'mainTranscript': struct { biotype: str, canonical: int32, category: str, cdna_start: int32, cdna_end: int32, codons: str, gene_id: str, gene_symbol: str, hgvs: str, hgvsc: str, major_consequence: str, major_consequence_rank: int32, transcript_id: str, amino_acids: str, domains: str, hgvsp: str, lof: str, lof_flags: str, lof_filter: str, lof_info: str, polyphen_prediction: str, protein_id: str, sift_prediction: str } 'mpc': struct { MPC: str } 'originalAltAlleles': array 'pos': int32 'primate_ai': struct { score: float64 } 'ref': str 'rsid': str 'samples_ab': struct { 0_to_5: set, 5_to_10: set, 10_to_15: set, 15_to_20: set, 20_to_25: set, 25_to_30: set, 30_to_35: set, 35_to_40: set, 40_to_45: set } 'samples_gq': struct { 0_to_5: set, 5_to_10: set, 10_to_15: set, 15_to_20: set, 20_to_25: set, 25_to_30: set, 30_to_35: set, 35_to_40: set, 40_to_45: set, 45_to_50: set, 50_to_55: set, 55_to_60: set, 60_to_65: set, 65_to_70: set, 70_to_75: set, 75_to_80: set, 80_to_85: set, 85_to_90: set, 90_to_95: set } 'samples_no_call': set 'samples_num_alt': struct { 1: set, 2: set } 'sortedTranscriptConsequences': array, domains: array, major_consequence: str, category: str, hgvs: str, major_consequence_rank: int32, transcript_rank: int32 }> 'splice_ai': struct { delta_score: float32 } 'start': int32 'topmed': struct { AC: int32, AF: float64, AN: int32, Hom: int32, Het: int32 } 'transcriptConsequenceTerms': set 'transcriptIds': set 'utrVariantAnnotation': array 'variantId': str 'vep': struct { assembly_name: str, allele_string: str, ancestral: str, colocated_variants: array, end: int32, eas_allele: str, eas_maf: float64, ea_allele: str, ea_maf: float64, eur_allele: str, eur_maf: float64, exac_adj_allele: str, exac_adj_maf: float64, exac_allele: str, exac_afr_allele: str, exac_afr_maf: float64, exac_amr_allele: str, exac_amr_maf: float64, exac_eas_allele: str, exac_eas_maf: float64, exac_fin_allele: str, exac_fin_maf: float64, exac_maf: float64, exac_nfe_allele: str, exac_nfe_maf: float64, exac_oth_allele: str, exac_oth_maf: float64, exac_sas_allele: str, exac_sas_maf: float64, id: str, minor_allele: str, minor_allele_freq: float64, phenotype_or_disease: int32, pubmed: array, sas_allele: str, sas_maf: float64, somatic: int32, start: int32, strand: int32 }>, context: str, end: int32, id: str, input: str, intergenic_consequences: array, impact: str, minimised: int32, variant_allele: str }>, most_severe_consequence: str, motif_feature_consequences: array, high_inf_pos: str, impact: str, minimised: int32, motif_feature_id: str, motif_name: str, motif_pos: int32, motif_score_change: float64, strand: int32, variant_allele: str }>, regulatory_feature_consequences: array, impact: str, minimised: int32, regulatory_feature_id: str, variant_allele: str }>, seq_region_name: str, start: int32, strand: int32, transcript_consequences: array, distance: int32, domains: array, exon: str, gene_id: str, gene_pheno: int32, gene_symbol: str, gene_symbol_source: str, hgnc_id: str, hgvsc: str, hgvsp: str, hgvs_offset: int32, impact: str, intron: str, lof: str, lof_flags: str, lof_filter: str, lof_info: str, minimised: int32, polyphen_prediction: str, polyphen_score: float64, protein_end: int32, protein_start: int32, protein_id: str, sift_prediction: str, sift_score: float64, strand: int32, swissprot: str, transcript_id: str, trembl: str, tsl: int32, uniparc: str, variant_allele: str }>, variant_class: str } 'xpos': int64 'xstart': int64 'xstop': int64 ---------------------------------------- Entry fields: 'AD': array 'DP': int32 'GQ': int32 'GT': call 'MIN_DP': int32 'PGT': call 'PID': str 'PL': array 'PS': int32 'RGQ': int32 'SB': array ---------------------------------------- Column key: ['s'] Row key: ['locus', 'alleles'] ---------------------------------------- [Stage 1:================================> (632 + 193) / 1000] [Stage 1:=====================================================>(993 + 7) / 1000]2022-05-31 16:35:15 Hail: INFO: Coerced almost-sorted dataset [Stage 2:> (0 + 12) / 12] [Stage 2:====> (1 + 11) / 12] [Stage 2:=========> (2 + 10) / 12] [Stage 2:==============> (3 + 9) / 12] [Stage 2:===================> (4 + 8) / 12] [Stage 2:=============================> (6 + 6) / 12] [Stage 2:======================================> (8 + 4) / 12] [Stage 2:===========================================> (9 + 3) / 12] [Stage 2:===============================================> (10 + 2) / 12] [Stage 2:====================================================> (11 + 1) / 12] [Stage 3:=======================================> (752 + 193) / 1000]2022-05-31 16:35:31 Hail: WARN: coalesced to 792 partitions, less than requested 1000 [Stage 5:> (0 + 0) / 792] [Stage 5:> (0 + 74) / 792] [Stage 5:> (0 + 174) / 792] [Stage 5:> (0 + 192) / 792] [Stage 5:> (1 + 192) / 792] [Stage 5:=> (22 + 192) / 792] [Stage 5:==> (37 + 192) / 792] [Stage 5:==> (39 + 192) / 792] [Stage 5:===> (58 + 193) / 792] [Stage 5:====> (68 + 192) / 792] [Stage 5:====> (70 + 192) / 792] [Stage 5:====> (73 + 192) / 792] [Stage 5:=====> (76 + 192) / 792] [Stage 5:=====> (79 + 192) / 792] [Stage 5:=====> (80 + 192) / 792] [Stage 5:======> (100 + 192) / 792] [Stage 5:======> (102 + 192) / 792] [Stage 5:=======> (105 + 192) / 792] [Stage 5:========> (125 + 192) / 792] [Stage 5:=========> (137 + 192) / 792] [Stage 5:=========> (140 + 192) / 792] [Stage 5:=========> (144 + 192) / 792] [Stage 5:=========> (146 + 192) / 792] [Stage 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