基因数据处理109之SparkBWA运行成功的部分log

原创

KeepLearningAI 2023-01-04 11:00:19 ©著作权

文章标签 spark adam 基因数据处理 hadoop Java 文章分类 运维

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数据来自：

http://219.219.220.149:18080/history/application_1466866953605_0001/executors/

http://219.219.220.248:8042/node/containerlogs/container_1466866953605_0001_01_000003/hadoop/stderr/?start=0

SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/home/hadoop/cloud/workspace/tmp/nm-local-dir/usercache/hadoop/filecache/10/spark-assembly-1.5.2-hadoop2.6.0.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/hadoop/cloud/hadoop-2.6.0/share/hadoop/common/lib/slf4j-log4j12-1.7.5.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]
16/06/25 23:28:05 INFO executor.CoarseGrainedExecutorBackend: Registered signal handlers for [TERM, HUP, INT]
16/06/25 23:28:06 WARN util.NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
16/06/25 23:28:06 INFO spark.SecurityManager: Changing view acls to: hadoop
16/06/25 23:28:06 INFO spark.SecurityManager: Changing modify acls to: hadoop
16/06/25 23:28:06 INFO spark.SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(hadoop); users with modify permissions: Set(hadoop)
16/06/25 23:28:07 INFO slf4j.Slf4jLogger: Slf4jLogger started
16/06/25 23:28:07 INFO Remoting: Starting remoting
16/06/25 23:28:07 INFO Remoting: Remoting started; listening on addresses :[akka.tcp://driverPropsFetcher@Mcnode2:53394]
16/06/25 23:28:07 INFO util.Utils: Successfully started service 'driverPropsFetcher' on port 53394.
16/06/25 23:28:08 INFO spark.SecurityManager: Changing view acls to: hadoop
16/06/25 23:28:08 INFO spark.SecurityManager: Changing modify acls to: hadoop
16/06/25 23:28:08 INFO spark.SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users with view permissions: Set(hadoop); users with modify permissions: Set(hadoop)
16/06/25 23:28:08 INFO remote.RemoteActorRefProvider$RemotingTerminator: Shutting down remote daemon.
16/06/25 23:28:08 INFO remote.RemoteActorRefProvider$RemotingTerminator: Remote daemon shut down; proceeding with flushing remote transports.
16/06/25 23:28:08 INFO remote.RemoteActorRefProvider$RemotingTerminator: Remoting shut down.
16/06/25 23:28:08 INFO slf4j.Slf4jLogger: Slf4jLogger started
16/06/25 23:28:08 INFO Remoting: Starting remoting
16/06/25 23:28:08 INFO Remoting: Remoting started; listening on addresses :[akka.tcp://sparkExecutor@Mcnode2:56481]
16/06/25 23:28:08 INFO util.Utils: Successfully started service 'sparkExecutor' on port 56481.
16/06/25 23:28:08 INFO storage.DiskBlockManager: Created local directory at /home/hadoop/cloud/workspace/tmp/nm-local-dir/usercache/hadoop/appcache/application_1466866953605_0001/blockmgr-cdbd5c40-dbcb-4125-bbb5-e08e828fdc6d
16/06/25 23:28:08 INFO storage.MemoryStore: MemoryStore started with capacity 2.1 GB
16/06/25 23:28:08 INFO executor.CoarseGrainedExecutorBackend: Connecting to driver: akka.tcp://sparkDriver@219.219.220.149:34876/user/CoarseGrainedScheduler
16/06/25 23:28:08 INFO executor.CoarseGrainedExecutorBackend: Successfully registered with driver
16/06/25 23:28:08 INFO executor.Executor: Starting executor ID 1 on host Mcnode2
16/06/25 23:28:08 INFO util.Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 53069.
16/06/25 23:28:08 INFO netty.NettyBlockTransferService: Server created on 53069
16/06/25 23:28:08 INFO storage.BlockManagerMaster: Trying to register BlockManager
16/06/25 23:28:08 INFO storage.BlockManagerMaster: Registered BlockManager
16/06/25 23:28:08 INFO executor.CoarseGrainedExecutorBackend: Got assigned task 0
16/06/25 23:28:08 INFO executor.Executor: Running task 0.0 in stage 0.0 (TID 0)
16/06/25 23:28:08 INFO executor.Executor: Fetching http://219.219.220.149:49344/jars/SparkBWA.jar with timestamp 1466868430534
16/06/25 23:28:09 INFO util.Utils: Fetching http://219.219.220.149:49344/jars/SparkBWA.jar to /home/hadoop/cloud/workspace/tmp/nm-local-dir/usercache/hadoop/appcache/application_1466866953605_0001/spark-1755b7f0-a414-4e4c-ab0a-ba6eb1ae2e1c/fetchFileTemp4557595424669144985.tmp
16/06/25 23:28:09 INFO util.Utils: Copying /home/hadoop/cloud/workspace/tmp/nm-local-dir/usercache/hadoop/appcache/application_1466866953605_0001/spark-1755b7f0-a414-4e4c-ab0a-ba6eb1ae2e1c/-20723091621466868430534_cache to /home/hadoop/cloud/workspace/tmp/nm-local-dir/usercache/hadoop/appcache/application_1466866953605_0001/container_1466866953605_0001_01_000003/./SparkBWA.jar
16/06/25 23:28:09 INFO executor.Executor: Adding file:/home/hadoop/cloud/workspace/tmp/nm-local-dir/usercache/hadoop/appcache/application_1466866953605_0001/container_1466866953605_0001_01_000003/./SparkBWA.jar to class loader
16/06/25 23:28:09 INFO broadcast.TorrentBroadcast: Started reading broadcast variable 2
16/06/25 23:28:09 INFO storage.MemoryStore: ensureFreeSpace(1289) called with curMem=0, maxMem=2223023063
16/06/25 23:28:09 INFO storage.MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 1289.0 B, free 2.1 GB)
16/06/25 23:28:09 INFO broadcast.TorrentBroadcast: Reading broadcast variable 2 took 311 ms
16/06/25 23:28:09 INFO storage.MemoryStore: ensureFreeSpace(2136) called with curMem=1289, maxMem=2223023063
16/06/25 23:28:09 INFO storage.MemoryStore: Block broadcast_2 stored as values in memory (estimated size 2.1 KB, free 2.1 GB)
16/06/25 23:28:09 INFO rdd.NewHadoopRDD: Input split: hdfs://Master:9000/xubo/alignment/sparkBWA/g38L50c10000Nhs20Paired2.fastq:0+1085189
16/06/25 23:28:09 INFO broadcast.TorrentBroadcast: Started reading broadcast variable 1
16/06/25 23:28:09 INFO storage.MemoryStore: ensureFreeSpace(20491) called with curMem=3425, maxMem=2223023063
16/06/25 23:28:09 INFO storage.MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 20.0 KB, free 2.1 GB)
16/06/25 23:28:09 INFO broadcast.TorrentBroadcast: Reading broadcast variable 1 took 19 ms
16/06/25 23:28:09 INFO storage.MemoryStore: ensureFreeSpace(324048) called with curMem=23916, maxMem=2223023063
16/06/25 23:28:09 INFO storage.MemoryStore: Block broadcast_1 stored as values in memory (estimated size 316.5 KB, free 2.1 GB)
16/06/25 23:28:10 INFO executor.Executor: Finished task 0.0 in stage 0.0 (TID 0). 2244 bytes result sent to driver
16/06/25 23:28:13 INFO executor.CoarseGrainedExecutorBackend: Got assigned task 3
16/06/25 23:28:13 INFO executor.Executor: Running task 0.0 in stage 3.0 (TID 3)
16/06/25 23:28:13 INFO spark.MapOutputTrackerWorker: Updating epoch to 3 and clearing cache
16/06/25 23:28:13 INFO broadcast.TorrentBroadcast: Started reading broadcast variable 5
16/06/25 23:28:13 INFO storage.MemoryStore: ensureFreeSpace(2450) called with curMem=347964, maxMem=2223023063
16/06/25 23:28:13 INFO storage.MemoryStore: Block broadcast_5_piece0 stored as bytes in memory (estimated size 2.4 KB, free 2.1 GB)
16/06/25 23:28:13 INFO broadcast.TorrentBroadcast: Reading broadcast variable 5 took 15 ms
16/06/25 23:28:13 INFO storage.MemoryStore: ensureFreeSpace(4240) called with curMem=350414, maxMem=2223023063
16/06/25 23:28:13 INFO storage.MemoryStore: Block broadcast_5 stored as values in memory (estimated size 4.1 KB, free 2.1 GB)
16/06/25 23:28:13 INFO spark.CacheManager: Partition rdd_9_0 not found, computing it
16/06/25 23:28:13 INFO spark.MapOutputTrackerWorker: Don't have map outputs for shuffle 2, fetching them
16/06/25 23:28:13 INFO spark.MapOutputTrackerWorker: Doing the fetch; tracker endpoint = AkkaRpcEndpointRef(Actor[akka.tcp://sparkDriver@219.219.220.149:34876/user/MapOutputTracker#612302847])
16/06/25 23:28:13 INFO spark.MapOutputTrackerWorker: Got the output locations
16/06/25 23:28:13 INFO storage.ShuffleBlockFetcherIterator: Getting 1 non-empty blocks out of 1 blocks
16/06/25 23:28:13 INFO storage.ShuffleBlockFetcherIterator: Started 1 remote fetches in 11 ms
16/06/25 23:28:13 INFO storage.MemoryStore: ensureFreeSpace(752944) called with curMem=354654, maxMem=2223023063
16/06/25 23:28:13 INFO storage.MemoryStore: Block rdd_9_0 stored as values in memory (estimated size 735.3 KB, free 2.1 GB)
16/06/25 23:28:13 INFO BwaInterpreter: JMAbuin:: Writing file: /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD0_1
16/06/25 23:28:13 INFO BwaInterpreter: JMAbuin:: Writing file: /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD0_2
[Java_BwaJni_bwa_1jni] Arg 0 'bwa'
[Java_BwaJni_bwa_1jni] Algorithm found 1 'mem'
[Java_BwaJni_bwa_1jni] Arg 1 'mem'
[Java_BwaJni_bwa_1jni] Filename parameter -f found 2 '-f'
[Java_BwaJni_bwa_1jni] Arg 2 '-f'
[Java_BwaJni_bwa_1jni] Filename found 3 '/home/hadoop/cloud/workspace/tmpSparkBWA_g38L50c10000Nhs20Paired1.fastq-7-NoSort-application_1466866953605_0001-0.sam'
[Java_BwaJni_bwa_1jni] Arg 3 '/home/hadoop/cloud/workspace/tmpSparkBWA_g38L50c10000Nhs20Paired1.fastq-7-NoSort-application_1466866953605_0001-0.sam'
[Java_BwaJni_bwa_1jni] Arg 4 '/home/hadoop/xubo/ref/GRCH38L1Index/GRCH38chr1L3556522.fasta'
[Java_BwaJni_bwa_1jni] Arg 5 '/home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD0_1'
[Java_BwaJni_bwa_1jni] Arg 6 '/home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD0_2'
[Java_BwaJni_bwa_1jni] option[0]: bwa.
[Java_BwaJni_bwa_1jni] option[1]: mem.
[Java_BwaJni_bwa_1jni] option[2]: /home/hadoop/xubo/ref/GRCH38L1Index/GRCH38chr1L3556522.fasta.
[Java_BwaJni_bwa_1jni] option[3]: /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD0_1.
[Java_BwaJni_bwa_1jni] option[4]: /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD0_2.
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2640 sequences (132000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 1078, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (192, 198, 205)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (166, 231)
[M::mem_pestat] mean and std.dev: (198.56, 9.68)
[M::mem_pestat] low and high boundaries for proper pairs: (153, 244)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 2640 reads in 0.447 CPU sec, 0.480 real sec
[main] Version: 0.7.12-r1044
[main] CMD: bwa mem /home/hadoop/xubo/ref/GRCH38L1Index/GRCH38chr1L3556522.fasta /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD0_1 /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD0_2
[main] Real time: 8.008 sec; CPU: 10.281 sec
[Java_BwaJni_bwa_1jni] Return code from BWA 0.
16/06/25 23:28:22 INFO executor.Executor: Finished task 0.0 in stage 3.0 (TID 3). 1908 bytes result sent to driver
16/06/25 23:28:22 INFO executor.CoarseGrainedExecutorBackend: Got assigned task 8
16/06/25 23:28:22 INFO executor.Executor: Running task 5.0 in stage 3.0 (TID 8)
16/06/25 23:28:22 INFO spark.CacheManager: Partition rdd_9_5 not found, computing it
16/06/25 23:28:22 INFO storage.ShuffleBlockFetcherIterator: Getting 1 non-empty blocks out of 1 blocks
16/06/25 23:28:22 INFO storage.ShuffleBlockFetcherIterator: Started 1 remote fetches in 2 ms
16/06/25 23:28:22 INFO storage.MemoryStore: ensureFreeSpace(754336) called with curMem=1107598, maxMem=2223023063
16/06/25 23:28:22 INFO storage.MemoryStore: Block rdd_9_5 stored as values in memory (estimated size 736.7 KB, free 2.1 GB)
16/06/25 23:28:22 INFO BwaInterpreter: JMAbuin:: Writing file: /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD5_1
16/06/25 23:28:22 INFO BwaInterpreter: JMAbuin:: Writing file: /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD5_2
[Java_BwaJni_bwa_1jni] Arg 0 'bwa'
[Java_BwaJni_bwa_1jni] Algorithm found 1 'mem'
[Java_BwaJni_bwa_1jni] Arg 1 'mem'
[Java_BwaJni_bwa_1jni] Filename parameter -f found 2 '-f'
[Java_BwaJni_bwa_1jni] Arg 2 '-f'
[Java_BwaJni_bwa_1jni] Filename found 3 '/home/hadoop/cloud/workspace/tmpSparkBWA_g38L50c10000Nhs20Paired1.fastq-7-NoSort-application_1466866953605_0001-5.sam'
[Java_BwaJni_bwa_1jni] Arg 3 '/home/hadoop/cloud/workspace/tmpSparkBWA_g38L50c10000Nhs20Paired1.fastq-7-NoSort-application_1466866953605_0001-5.sam'
[Java_BwaJni_bwa_1jni] Arg 4 '/home/hadoop/xubo/ref/GRCH38L1Index/GRCH38chr1L3556522.fasta'
[Java_BwaJni_bwa_1jni] Arg 5 '/home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD5_1'
[Java_BwaJni_bwa_1jni] Arg 6 '/home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD5_2'
[Java_BwaJni_bwa_1jni] option[0]: bwa.
[Java_BwaJni_bwa_1jni] option[1]: mem.
[Java_BwaJni_bwa_1jni] option[2]: /home/hadoop/xubo/ref/GRCH38L1Index/GRCH38chr1L3556522.fasta.
[Java_BwaJni_bwa_1jni] option[3]: /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD5_1.
[Java_BwaJni_bwa_1jni] option[4]: /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD5_2.
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2640 sequences (132000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 1069, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (192, 199, 206)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (164, 234)
[M::mem_pestat] mean and std.dev: (199.09, 10.15)
[M::mem_pestat] low and high boundaries for proper pairs: (150, 248)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 2640 reads in 0.570 CPU sec, 0.490 real sec
[main] Version: 0.7.12-r1044
[main] CMD: bwa mem /home/hadoop/xubo/ref/GRCH38L1Index/GRCH38chr1L3556522.fasta /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD5_1 /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD5_2
[main] Real time: 0.790 sec; CPU: 12.031 sec
[Java_BwaJni_bwa_1jni] Return code from BWA 0.
16/06/25 23:28:23 INFO executor.Executor: Finished task 5.0 in stage 3.0 (TID 8). 1908 bytes result sent to driver
16/06/25 23:28:23 INFO executor.CoarseGrainedExecutorBackend: Got assigned task 9
16/06/25 23:28:23 INFO executor.Executor: Running task 6.0 in stage 3.0 (TID 9)
16/06/25 23:28:23 INFO spark.CacheManager: Partition rdd_9_6 not found, computing it
16/06/25 23:28:23 INFO storage.ShuffleBlockFetcherIterator: Getting 1 non-empty blocks out of 1 blocks
16/06/25 23:28:23 INFO storage.ShuffleBlockFetcherIterator: Started 1 remote fetches in 1 ms
16/06/25 23:28:23 INFO storage.MemoryStore: ensureFreeSpace(752896) called with curMem=1861934, maxMem=2223023063
16/06/25 23:28:23 INFO storage.MemoryStore: Block rdd_9_6 stored as values in memory (estimated size 735.3 KB, free 2.1 GB)
16/06/25 23:28:23 INFO BwaInterpreter: JMAbuin:: Writing file: /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD6_1
16/06/25 23:28:23 INFO BwaInterpreter: JMAbuin:: Writing file: /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD6_2
[Java_BwaJni_bwa_1jni] Arg 0 'bwa'
[Java_BwaJni_bwa_1jni] Algorithm found 1 'mem'
[Java_BwaJni_bwa_1jni] Arg 1 'mem'
[Java_BwaJni_bwa_1jni] Filename parameter -f found 2 '-f'
[Java_BwaJni_bwa_1jni] Arg 2 '-f'
[Java_BwaJni_bwa_1jni] Filename found 3 '/home/hadoop/cloud/workspace/tmpSparkBWA_g38L50c10000Nhs20Paired1.fastq-7-NoSort-application_1466866953605_0001-6.sam'
[Java_BwaJni_bwa_1jni] Arg 3 '/home/hadoop/cloud/workspace/tmpSparkBWA_g38L50c10000Nhs20Paired1.fastq-7-NoSort-application_1466866953605_0001-6.sam'
[Java_BwaJni_bwa_1jni] Arg 4 '/home/hadoop/xubo/ref/GRCH38L1Index/GRCH38chr1L3556522.fasta'
[Java_BwaJni_bwa_1jni] Arg 5 '/home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD6_1'
[Java_BwaJni_bwa_1jni] Arg 6 '/home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD6_2'
[Java_BwaJni_bwa_1jni] option[0]: bwa.
[Java_BwaJni_bwa_1jni] option[1]: mem.
[Java_BwaJni_bwa_1jni] option[2]: /home/hadoop/xubo/ref/GRCH38L1Index/GRCH38chr1L3556522.fasta.
[Java_BwaJni_bwa_1jni] option[3]: /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD6_1.
[Java_BwaJni_bwa_1jni] option[4]: /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD6_2.
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 2640 sequences (132000 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 1032, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (192, 199, 205)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (166, 231)
[M::mem_pestat] mean and std.dev: (198.42, 10.13)
[M::mem_pestat] low and high boundaries for proper pairs: (153, 244)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 2640 reads in 0.563 CPU sec, 0.560 real sec
[main] Version: 0.7.12-r1044
[main] CMD: bwa mem /home/hadoop/xubo/ref/GRCH38L1Index/GRCH38chr1L3556522.fasta /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD6_1 /home/hadoop/cloud/workspace/tmpapplication_1466866953605_0001-RDD6_2
[main] Real time: 0.754 sec; CPU: 12.901 sec
[Java_BwaJni_bwa_1jni] Return code from BWA 0.
16/06/25 23:28:24 INFO executor.Executor: Finished task 6.0 in stage 3.0 (TID 9). 1908 bytes result sent to driver
16/06/25 23:28:24 INFO executor.CoarseGrainedExecutorBackend: Driver commanded a shutdown
16/06/25 23:28:24 INFO storage.MemoryStore: MemoryStore cleared
16/06/25 23:28:24 INFO storage.BlockManager: BlockManager stopped
16/06/25 23:28:25 INFO remote.RemoteActorRefProvider$RemotingTerminator: Shutting down remote daemon.
16/06/25 23:28:25 INFO remote.RemoteActorRefProvider$RemotingTerminator: Remote daemon shut down; proceeding with flushing remote transports.
16/06/25 23:28:25 INFO remote.RemoteActorRefProvider$RemotingTerminator: Remoting shut down.
16/06/25 23:28:25 INFO util.ShutdownHookManager: Shutdown hook called
16/06/25 23:28:25 INFO util.ShutdownHookManager: Deleting directory /home/hadoop/cloud/workspace/tmp/nm-local-dir/usercache/hadoop/appcache/application_1466866953605_0001/spark-1755b7f0-a414-4e4c-ab0a-ba6eb1ae2e1c

参考

【1】https://github.com/xubo245/AdamLearning
【2】https://github.com/bigdatagenomics/adam/ 
【4】http://spark.apache.org

研究成果：

【1】 [BIBM] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Chao Wang, and Xuehai Zhou, "Distributed Gene Clinical Decision Support System Based on Cloud Computing", in IEEE International Conference on Bioinformatics and Biomedicine. (BIBM 2017, CCF B)
【2】 [IEEE CLOUD] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Xuehai Zhou. Efficient Distributed Smith-Waterman Algorithm Based on Apache Spark (CLOUD 2017, CCF-C).
【3】 [CCGrid] Bo Xu, Changlong Li, Hang Zhuang, Jiali Wang, Qingfeng Wang, Jinhong Zhou, Xuehai Zhou. DSA: Scalable Distributed Sequence Alignment System Using SIMD Instructions. (CCGrid 2017, CCF-C).