Console Output

Skipping 2,148 KB.. Full Log
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
20/12/02 19:48:42 INFO SparkContext: Running Spark version 3.0.1
20/12/02 19:48:42 INFO ResourceUtils: ==============================================================
20/12/02 19:48:42 INFO ResourceUtils: Resources for spark.driver:

20/12/02 19:48:42 INFO ResourceUtils: ==============================================================
20/12/02 19:48:42 INFO SparkContext: Submitted application: transformAlignments
20/12/02 19:48:42 INFO SecurityManager: Changing view acls to: jenkins
20/12/02 19:48:42 INFO SecurityManager: Changing modify acls to: jenkins
20/12/02 19:48:42 INFO SecurityManager: Changing view acls groups to: 
20/12/02 19:48:42 INFO SecurityManager: Changing modify acls groups to: 
20/12/02 19:48:42 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(jenkins); groups with view permissions: Set(); users  with modify permissions: Set(jenkins); groups with modify permissions: Set()
20/12/02 19:48:42 INFO Utils: Successfully started service 'sparkDriver' on port 46661.
20/12/02 19:48:42 INFO SparkEnv: Registering MapOutputTracker
20/12/02 19:48:42 INFO SparkEnv: Registering BlockManagerMaster
20/12/02 19:48:42 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/12/02 19:48:42 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/12/02 19:48:42 INFO SparkEnv: Registering BlockManagerMasterHeartbeat
20/12/02 19:48:42 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-1e5fb51f-91e9-48de-aa1a-0fb6f3b1afb8
20/12/02 19:48:42 INFO MemoryStore: MemoryStore started with capacity 408.9 MiB
20/12/02 19:48:42 INFO SparkEnv: Registering OutputCommitCoordinator
20/12/02 19:48:43 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/12/02 19:48:43 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.122.1:4040
20/12/02 19:48:43 INFO SparkContext: Added JAR file:/tmp/adamTestyZdaqTT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar at spark://192.168.122.1:46661/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with timestamp 1606967323130
20/12/02 19:48:43 INFO Executor: Starting executor ID driver on host 192.168.122.1
20/12/02 19:48:43 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 37969.
20/12/02 19:48:43 INFO NettyBlockTransferService: Server created on 192.168.122.1:37969
20/12/02 19:48:43 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/12/02 19:48:43 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.122.1, 37969, None)
20/12/02 19:48:43 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.122.1:37969 with 408.9 MiB RAM, BlockManagerId(driver, 192.168.122.1, 37969, None)
20/12/02 19:48:43 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.122.1, 37969, None)
20/12/02 19:48:43 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.122.1, 37969, None)
20/12/02 19:48:43 INFO ADAMContext: Loading mouse_chrM.bam as BAM/CRAM/SAM and converting to Alignments.
20/12/02 19:48:43 INFO ADAMContext: Loaded header from file:/tmp/adamTestyZdaqTT/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam
20/12/02 19:48:44 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 289.9 KiB, free 408.6 MiB)
20/12/02 19:48:44 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 23.6 KiB, free 408.6 MiB)
20/12/02 19:48:44 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.122.1:37969 (size: 23.6 KiB, free: 408.9 MiB)
20/12/02 19:48:44 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:2054
20/12/02 19:48:46 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
20/12/02 19:48:46 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:48:46 INFO FileInputFormat: Total input paths to process : 1
20/12/02 19:48:46 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/12/02 19:48:46 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/12/02 19:48:46 INFO DAGScheduler: Final stage: ResultStage 0 (runJob at SparkHadoopWriter.scala:78)
20/12/02 19:48:46 INFO DAGScheduler: Parents of final stage: List()
20/12/02 19:48:46 INFO DAGScheduler: Missing parents: List()
20/12/02 19:48:46 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3805), which has no missing parents
20/12/02 19:48:46 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 84.5 KiB, free 408.5 MiB)
20/12/02 19:48:46 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 31.3 KiB, free 408.5 MiB)
20/12/02 19:48:46 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.122.1:37969 (size: 31.3 KiB, free: 408.8 MiB)
20/12/02 19:48:46 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1223
20/12/02 19:48:46 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3805) (first 15 tasks are for partitions Vector(0))
20/12/02 19:48:46 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/12/02 19:48:46 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, 192.168.122.1, executor driver, partition 0, PROCESS_LOCAL, 7443 bytes)
20/12/02 19:48:46 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/12/02 19:48:46 INFO Executor: Fetching spark://192.168.122.1:46661/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with timestamp 1606967323130
20/12/02 19:48:46 INFO TransportClientFactory: Successfully created connection to /192.168.122.1:46661 after 28 ms (0 ms spent in bootstraps)
20/12/02 19:48:46 INFO Utils: Fetching spark://192.168.122.1:46661/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar to /tmp/spark-c089f1dc-0b51-45fe-9ffd-057cd3582758/userFiles-42ada30d-401f-44fa-9f58-f54352a9a216/fetchFileTemp5947469748159132859.tmp
20/12/02 19:48:46 INFO Executor: Adding file:/tmp/spark-c089f1dc-0b51-45fe-9ffd-057cd3582758/userFiles-42ada30d-401f-44fa-9f58-f54352a9a216/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar to class loader
20/12/02 19:48:47 INFO NewHadoopRDD: Input split: file:/tmp/adamTestyZdaqTT/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam:83361792-833134657535
20/12/02 19:48:47 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:48:47 INFO CodecConfig: Compression: GZIP
20/12/02 19:48:47 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:48:47 INFO ParquetOutputFormat: Parquet block size to 134217728
20/12/02 19:48:47 INFO ParquetOutputFormat: Parquet page size to 1048576
20/12/02 19:48:47 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/12/02 19:48:47 INFO ParquetOutputFormat: Dictionary is on
20/12/02 19:48:47 INFO ParquetOutputFormat: Validation is off
20/12/02 19:48:47 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/12/02 19:48:47 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/12/02 19:48:47 INFO ParquetOutputFormat: Page size checking is: estimated
20/12/02 19:48:47 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/12/02 19:48:47 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/12/02 19:48:47 INFO CodecPool: Got brand-new compressor [.gz]
Ignoring SAM validation error: ERROR: Record 162622, Read name 613F0AAXX100423:3:58:9979:16082, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162624, Read name 613F0AAXX100423:6:13:3141:11793, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162625, Read name 613F0AAXX100423:8:39:18592:13552, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162635, Read name 613F1AAXX100423:7:2:13114:10698, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162637, Read name 613F1AAXX100423:6:100:8840:11167, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162639, Read name 613F1AAXX100423:8:15:10944:11181, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162640, Read name 613F1AAXX100423:8:17:5740:10104, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162651, Read name 613F1AAXX100423:1:53:11097:8261, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162654, Read name 613F1AAXX100423:2:112:16779:19612, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162657, Read name 613F0AAXX100423:8:28:7084:17683, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162659, Read name 613F0AAXX100423:8:39:19796:12794, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162662, Read name 613F1AAXX100423:5:116:9339:3264, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162667, Read name 613F0AAXX100423:4:67:2015:3054, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162669, Read name 613F0AAXX100423:7:7:11297:11738, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162674, Read name 613F0AAXX100423:6:59:10490:20829, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162678, Read name 613F1AAXX100423:8:11:17603:4766, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162682, Read name 613F0AAXX100423:5:86:10814:10257, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162683, Read name 613F0AAXX100423:5:117:14178:6111, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162685, Read name 613F0AAXX100423:2:3:13563:6720, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162689, Read name 613F0AAXX100423:7:59:16009:15799, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162696, Read name 613F0AAXX100423:5:31:9663:18252, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162698, Read name 613F1AAXX100423:2:27:12264:14626, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162699, Read name 613F0AAXX100423:1:120:19003:6647, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162702, Read name 613F1AAXX100423:3:37:6972:18407, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162704, Read name 613F1AAXX100423:3:77:6946:3880, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162706, Read name 613F0AAXX100423:7:48:2692:3492, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162708, Read name 613F1AAXX100423:7:80:8790:1648, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162710, Read name 6141AAAXX100423:5:30:15036:17610, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162712, Read name 613F1AAXX100423:8:80:6261:4465, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162713, Read name 6141AAAXX100423:5:74:5542:6195, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162715, Read name 613F1AAXX100423:5:14:14844:13639, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162718, Read name 613F1AAXX100423:7:112:14569:8480, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162725, Read name 613F1AAXX100423:4:56:10160:9879, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162727, Read name 6141AAAXX100423:7:89:12209:9221, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162731, Read name 6141AAAXX100423:6:55:1590:19793, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162732, Read name 6141AAAXX100423:7:102:16679:12368, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162734, Read name 613F1AAXX100423:2:7:4909:18472, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162737, Read name 6141AAAXX100423:4:73:6574:10572, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162741, Read name 6141AAAXX100423:1:8:14113:12655, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162743, Read name 6141AAAXX100423:3:40:7990:5056, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162744, Read name 6141AAAXX100423:4:36:15793:3411, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162745, Read name 6141AAAXX100423:8:83:1139:18985, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162746, Read name 6141AAAXX100423:5:7:18196:13562, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162748, Read name 6141AAAXX100423:3:114:5639:7123, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162751, Read name 6141AAAXX100423:7:47:4898:8640, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162753, Read name 6141AAAXX100423:3:64:8064:8165, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162756, Read name 613F1AAXX100423:1:105:14386:1684, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162757, Read name 613F1AAXX100423:6:98:1237:19470, MAPQ should be 0 for unmapped read.
Ignoring SAM validation error: ERROR: Record 162761, Read name 613F1AAXX100423:7:106:19658:9261, MAPQ should be 0 for unmapped read.
20/12/02 19:48:53 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16043959
20/12/02 19:48:53 INFO FileOutputCommitter: Saved output of task 'attempt_20201202194846_0002_r_000000_0' to file:/tmp/adamTestyZdaqTT/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/_temporary/0/task_20201202194846_0002_r_000000
20/12/02 19:48:53 INFO SparkHadoopMapRedUtil: attempt_20201202194846_0002_r_000000_0: Committed
20/12/02 19:48:53 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 1021 bytes result sent to driver
20/12/02 19:48:53 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 7355 ms on 192.168.122.1 (executor driver) (1/1)
20/12/02 19:48:53 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/12/02 19:48:53 INFO DAGScheduler: ResultStage 0 (runJob at SparkHadoopWriter.scala:78) finished in 7.480 s
20/12/02 19:48:53 INFO DAGScheduler: Job 0 is finished. Cancelling potential speculative or zombie tasks for this job
20/12/02 19:48:53 INFO TaskSchedulerImpl: Killing all running tasks in stage 0: Stage finished
20/12/02 19:48:53 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 7.544476 s
20/12/02 19:48:53 INFO ParquetFileReader: Initiating action with parallelism: 5
20/12/02 19:48:53 INFO SparkHadoopWriter: Job job_20201202194846_0002 committed.
20/12/02 19:48:53 INFO SparkContext: Invoking stop() from shutdown hook
20/12/02 19:48:53 INFO SparkUI: Stopped Spark web UI at http://192.168.122.1:4040
20/12/02 19:48:53 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/12/02 19:48:53 INFO MemoryStore: MemoryStore cleared
20/12/02 19:48:53 INFO BlockManager: BlockManager stopped
20/12/02 19:48:53 INFO BlockManagerMaster: BlockManagerMaster stopped
20/12/02 19:48:54 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/12/02 19:48:54 INFO SparkContext: Successfully stopped SparkContext
20/12/02 19:48:54 INFO ShutdownHookManager: Shutdown hook called
20/12/02 19:48:54 INFO ShutdownHookManager: Deleting directory /tmp/spark-f3364e9a-2826-44d3-9f97-bbe56803868e
20/12/02 19:48:54 INFO ShutdownHookManager: Deleting directory /tmp/spark-c089f1dc-0b51-45fe-9ffd-057cd3582758

# then, sort the BAM
echo "Converting BAM to ADAM read format with sorting"
+ echo 'Converting BAM to ADAM read format with sorting'
Converting BAM to ADAM read format with sorting
rm -rf ${SORTED_READS}
+ rm -rf mouse_chrM.bam.reads.sorted.adam
${ADAM} transformAlignments -sort_by_reference_position ${READS} ${SORTED_READS}
+ ./bin/adam-submit transformAlignments -sort_by_reference_position mouse_chrM.bam.reads.adam mouse_chrM.bam.reads.sorted.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/tmp/adamTestyZdaqTT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/bin/spark-submit
20/12/02 19:48:55 WARN Utils: Your hostname, research-jenkins-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.122.1 instead (on interface virbr0)
20/12/02 19:48:55 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/12/02 19:48:55 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.ADAMMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
20/12/02 19:48:56 INFO SparkContext: Running Spark version 3.0.1
20/12/02 19:48:56 INFO ResourceUtils: ==============================================================
20/12/02 19:48:56 INFO ResourceUtils: Resources for spark.driver:

20/12/02 19:48:56 INFO ResourceUtils: ==============================================================
20/12/02 19:48:56 INFO SparkContext: Submitted application: transformAlignments
20/12/02 19:48:56 INFO SecurityManager: Changing view acls to: jenkins
20/12/02 19:48:56 INFO SecurityManager: Changing modify acls to: jenkins
20/12/02 19:48:56 INFO SecurityManager: Changing view acls groups to: 
20/12/02 19:48:56 INFO SecurityManager: Changing modify acls groups to: 
20/12/02 19:48:56 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(jenkins); groups with view permissions: Set(); users  with modify permissions: Set(jenkins); groups with modify permissions: Set()
20/12/02 19:48:56 INFO Utils: Successfully started service 'sparkDriver' on port 39345.
20/12/02 19:48:56 INFO SparkEnv: Registering MapOutputTracker
20/12/02 19:48:56 INFO SparkEnv: Registering BlockManagerMaster
20/12/02 19:48:56 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/12/02 19:48:56 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/12/02 19:48:56 INFO SparkEnv: Registering BlockManagerMasterHeartbeat
20/12/02 19:48:56 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-7e7eb9b6-499b-4995-8ddb-a9d5718bba7d
20/12/02 19:48:56 INFO MemoryStore: MemoryStore started with capacity 408.9 MiB
20/12/02 19:48:56 INFO SparkEnv: Registering OutputCommitCoordinator
20/12/02 19:48:56 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/12/02 19:48:57 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.122.1:4040
20/12/02 19:48:57 INFO SparkContext: Added JAR file:/tmp/adamTestyZdaqTT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar at spark://192.168.122.1:39345/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with timestamp 1606967337031
20/12/02 19:48:57 INFO Executor: Starting executor ID driver on host 192.168.122.1
20/12/02 19:48:57 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 33205.
20/12/02 19:48:57 INFO NettyBlockTransferService: Server created on 192.168.122.1:33205
20/12/02 19:48:57 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/12/02 19:48:57 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.122.1, 33205, None)
20/12/02 19:48:57 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.122.1:33205 with 408.9 MiB RAM, BlockManagerId(driver, 192.168.122.1, 33205, None)
20/12/02 19:48:57 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.122.1, 33205, None)
20/12/02 19:48:57 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.122.1, 33205, None)
20/12/02 19:48:57 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/12/02 19:48:59 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/12/02 19:48:59 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 309.3 KiB, free 408.6 MiB)
20/12/02 19:48:59 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.9 KiB, free 408.6 MiB)
20/12/02 19:48:59 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.122.1:33205 (size: 27.9 KiB, free: 408.9 MiB)
20/12/02 19:48:59 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1797
20/12/02 19:48:59 INFO TransformAlignments: Sorting alignments by reference position, with references ordered by name
20/12/02 19:48:59 INFO RDDBoundAlignmentDataset: Sorting alignments by reference position
20/12/02 19:49:00 INFO FileInputFormat: Total input paths to process : 1
20/12/02 19:49:00 INFO ParquetInputFormat: Total input paths to process : 1
20/12/02 19:49:00 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
20/12/02 19:49:00 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:49:00 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/12/02 19:49:00 INFO DAGScheduler: Registering RDD 2 (sortBy at AlignmentDataset.scala:1010) as input to shuffle 0
20/12/02 19:49:00 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/12/02 19:49:00 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
20/12/02 19:49:00 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
20/12/02 19:49:00 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
20/12/02 19:49:00 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentDataset.scala:1010), which has no missing parents
20/12/02 19:49:00 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 6.9 KiB, free 408.6 MiB)
20/12/02 19:49:00 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 4.0 KiB, free 408.6 MiB)
20/12/02 19:49:00 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.122.1:33205 (size: 4.0 KiB, free: 408.9 MiB)
20/12/02 19:49:00 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1223
20/12/02 19:49:00 INFO DAGScheduler: Submitting 1 missing tasks from ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentDataset.scala:1010) (first 15 tasks are for partitions Vector(0))
20/12/02 19:49:00 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/12/02 19:49:00 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, 192.168.122.1, executor driver, partition 0, PROCESS_LOCAL, 7482 bytes)
20/12/02 19:49:00 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/12/02 19:49:00 INFO Executor: Fetching spark://192.168.122.1:39345/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with timestamp 1606967337031
20/12/02 19:49:00 INFO TransportClientFactory: Successfully created connection to /192.168.122.1:39345 after 33 ms (0 ms spent in bootstraps)
20/12/02 19:49:00 INFO Utils: Fetching spark://192.168.122.1:39345/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar to /tmp/spark-dbe9e0ac-c29f-4b59-ada0-06581781aa7a/userFiles-94255feb-2440-48d6-850e-c01c8cc41d52/fetchFileTemp7572736484862546626.tmp
20/12/02 19:49:00 INFO Executor: Adding file:/tmp/spark-dbe9e0ac-c29f-4b59-ada0-06581781aa7a/userFiles-94255feb-2440-48d6-850e-c01c8cc41d52/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar to class loader
20/12/02 19:49:01 INFO NewHadoopRDD: Input split: file:/tmp/adamTestyZdaqTT/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/12/02 19:49:01 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/12/02 19:49:01 INFO InternalParquetRecordReader: at row 0. reading next block
20/12/02 19:49:01 INFO CodecPool: Got brand-new decompressor [.gz]
20/12/02 19:49:01 INFO InternalParquetRecordReader: block read in memory in 40 ms. row count = 163064
20/12/02 19:49:03 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 1086 bytes result sent to driver
20/12/02 19:49:03 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3548 ms on 192.168.122.1 (executor driver) (1/1)
20/12/02 19:49:03 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/12/02 19:49:03 INFO DAGScheduler: ShuffleMapStage 0 (sortBy at AlignmentDataset.scala:1010) finished in 3.679 s
20/12/02 19:49:03 INFO DAGScheduler: looking for newly runnable stages
20/12/02 19:49:03 INFO DAGScheduler: running: Set()
20/12/02 19:49:03 INFO DAGScheduler: waiting: Set(ResultStage 1)
20/12/02 19:49:03 INFO DAGScheduler: failed: Set()
20/12/02 19:49:03 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3805), which has no missing parents
20/12/02 19:49:03 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 86.0 KiB, free 408.5 MiB)
20/12/02 19:49:03 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 32.2 KiB, free 408.4 MiB)
20/12/02 19:49:03 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.122.1:33205 (size: 32.2 KiB, free: 408.8 MiB)
20/12/02 19:49:03 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1223
20/12/02 19:49:03 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3805) (first 15 tasks are for partitions Vector(0))
20/12/02 19:49:03 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
20/12/02 19:49:03 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, 192.168.122.1, executor driver, partition 0, NODE_LOCAL, 7143 bytes)
20/12/02 19:49:03 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
20/12/02 19:49:04 INFO ShuffleBlockFetcherIterator: Getting 1 (24.5 MiB) non-empty blocks including 1 (24.5 MiB) local and 0 (0.0 B) host-local and 0 (0.0 B) remote blocks
20/12/02 19:49:04 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 9 ms
20/12/02 19:49:05 INFO BlockManagerInfo: Removed broadcast_1_piece0 on 192.168.122.1:33205 in memory (size: 4.0 KiB, free: 408.8 MiB)
20/12/02 19:49:06 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:49:06 INFO CodecConfig: Compression: GZIP
20/12/02 19:49:06 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:49:06 INFO ParquetOutputFormat: Parquet block size to 134217728
20/12/02 19:49:06 INFO ParquetOutputFormat: Parquet page size to 1048576
20/12/02 19:49:06 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/12/02 19:49:06 INFO ParquetOutputFormat: Dictionary is on
20/12/02 19:49:06 INFO ParquetOutputFormat: Validation is off
20/12/02 19:49:06 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/12/02 19:49:06 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/12/02 19:49:06 INFO ParquetOutputFormat: Page size checking is: estimated
20/12/02 19:49:06 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/12/02 19:49:06 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/12/02 19:49:06 INFO CodecPool: Got brand-new compressor [.gz]
20/12/02 19:49:09 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16004474
20/12/02 19:49:10 INFO FileOutputCommitter: Saved output of task 'attempt_20201202194900_0005_r_000000_0' to file:/tmp/adamTestyZdaqTT/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.sorted.adam/_temporary/0/task_20201202194900_0005_r_000000
20/12/02 19:49:10 INFO SparkHadoopMapRedUtil: attempt_20201202194900_0005_r_000000_0: Committed
20/12/02 19:49:10 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1408 bytes result sent to driver
20/12/02 19:49:10 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 6088 ms on 192.168.122.1 (executor driver) (1/1)
20/12/02 19:49:10 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
20/12/02 19:49:10 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 6.137 s
20/12/02 19:49:10 INFO DAGScheduler: Job 0 is finished. Cancelling potential speculative or zombie tasks for this job
20/12/02 19:49:10 INFO TaskSchedulerImpl: Killing all running tasks in stage 1: Stage finished
20/12/02 19:49:10 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 9.894907 s
20/12/02 19:49:10 INFO ParquetFileReader: Initiating action with parallelism: 5
20/12/02 19:49:10 INFO SparkHadoopWriter: Job job_20201202194900_0005 committed.
20/12/02 19:49:10 INFO SparkContext: Invoking stop() from shutdown hook
20/12/02 19:49:10 INFO SparkUI: Stopped Spark web UI at http://192.168.122.1:4040
20/12/02 19:49:10 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/12/02 19:49:10 INFO MemoryStore: MemoryStore cleared
20/12/02 19:49:10 INFO BlockManager: BlockManager stopped
20/12/02 19:49:10 INFO BlockManagerMaster: BlockManagerMaster stopped
20/12/02 19:49:10 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/12/02 19:49:10 INFO SparkContext: Successfully stopped SparkContext
20/12/02 19:49:10 INFO ShutdownHookManager: Shutdown hook called
20/12/02 19:49:10 INFO ShutdownHookManager: Deleting directory /tmp/spark-c519cd5b-1645-496c-b118-8dec15b51497
20/12/02 19:49:10 INFO ShutdownHookManager: Deleting directory /tmp/spark-dbe9e0ac-c29f-4b59-ada0-06581781aa7a

# convert the reads to fragments to re-pair the reads
echo "Converting read file to fragments"
+ echo 'Converting read file to fragments'
Converting read file to fragments
rm -rf ${FRAGMENTS}
+ rm -rf mouse_chrM.bam.fragments.adam
${ADAM} transformFragments -load_as_alignments ${READS} ${FRAGMENTS}
+ ./bin/adam-submit transformFragments -load_as_alignments mouse_chrM.bam.reads.adam mouse_chrM.bam.fragments.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/tmp/adamTestyZdaqTT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/bin/spark-submit
20/12/02 19:49:11 WARN Utils: Your hostname, research-jenkins-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.122.1 instead (on interface virbr0)
20/12/02 19:49:11 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/12/02 19:49:12 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.ADAMMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
20/12/02 19:49:12 INFO SparkContext: Running Spark version 3.0.1
20/12/02 19:49:12 INFO ResourceUtils: ==============================================================
20/12/02 19:49:12 INFO ResourceUtils: Resources for spark.driver:

20/12/02 19:49:12 INFO ResourceUtils: ==============================================================
20/12/02 19:49:12 INFO SparkContext: Submitted application: transformFragments
20/12/02 19:49:12 INFO SecurityManager: Changing view acls to: jenkins
20/12/02 19:49:12 INFO SecurityManager: Changing modify acls to: jenkins
20/12/02 19:49:12 INFO SecurityManager: Changing view acls groups to: 
20/12/02 19:49:12 INFO SecurityManager: Changing modify acls groups to: 
20/12/02 19:49:12 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(jenkins); groups with view permissions: Set(); users  with modify permissions: Set(jenkins); groups with modify permissions: Set()
20/12/02 19:49:12 INFO Utils: Successfully started service 'sparkDriver' on port 35201.
20/12/02 19:49:12 INFO SparkEnv: Registering MapOutputTracker
20/12/02 19:49:12 INFO SparkEnv: Registering BlockManagerMaster
20/12/02 19:49:12 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/12/02 19:49:12 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/12/02 19:49:12 INFO SparkEnv: Registering BlockManagerMasterHeartbeat
20/12/02 19:49:12 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-83ae5c9a-cbf2-481e-9a75-5bde16fdc473
20/12/02 19:49:13 INFO MemoryStore: MemoryStore started with capacity 408.9 MiB
20/12/02 19:49:13 INFO SparkEnv: Registering OutputCommitCoordinator
20/12/02 19:49:13 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/12/02 19:49:13 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.122.1:4040
20/12/02 19:49:13 INFO SparkContext: Added JAR file:/tmp/adamTestyZdaqTT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar at spark://192.168.122.1:35201/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with timestamp 1606967353351
20/12/02 19:49:13 INFO Executor: Starting executor ID driver on host 192.168.122.1
20/12/02 19:49:13 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 40251.
20/12/02 19:49:13 INFO NettyBlockTransferService: Server created on 192.168.122.1:40251
20/12/02 19:49:13 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/12/02 19:49:13 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.122.1, 40251, None)
20/12/02 19:49:13 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.122.1:40251 with 408.9 MiB RAM, BlockManagerId(driver, 192.168.122.1, 40251, None)
20/12/02 19:49:13 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.122.1, 40251, None)
20/12/02 19:49:13 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.122.1, 40251, None)
20/12/02 19:49:14 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/12/02 19:49:15 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/12/02 19:49:15 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 309.3 KiB, free 408.6 MiB)
20/12/02 19:49:16 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.9 KiB, free 408.6 MiB)
20/12/02 19:49:16 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.122.1:40251 (size: 27.9 KiB, free: 408.9 MiB)
20/12/02 19:49:16 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1797
20/12/02 19:49:16 INFO FileInputFormat: Total input paths to process : 1
20/12/02 19:49:16 INFO ParquetInputFormat: Total input paths to process : 1
20/12/02 19:49:16 INFO RDDBoundFragmentDataset: Saving data in ADAM format
20/12/02 19:49:16 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:49:16 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/12/02 19:49:16 INFO DAGScheduler: Registering RDD 2 (groupBy at SingleReadBucket.scala:97) as input to shuffle 0
20/12/02 19:49:16 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/12/02 19:49:16 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
20/12/02 19:49:16 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
20/12/02 19:49:16 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
20/12/02 19:49:16 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:97), which has no missing parents
20/12/02 19:49:16 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 7.4 KiB, free 408.6 MiB)
20/12/02 19:49:16 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 4.0 KiB, free 408.6 MiB)
20/12/02 19:49:16 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.122.1:40251 (size: 4.0 KiB, free: 408.9 MiB)
20/12/02 19:49:16 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1223
20/12/02 19:49:16 INFO DAGScheduler: Submitting 1 missing tasks from ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:97) (first 15 tasks are for partitions Vector(0))
20/12/02 19:49:16 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/12/02 19:49:16 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, 192.168.122.1, executor driver, partition 0, PROCESS_LOCAL, 7482 bytes)
20/12/02 19:49:16 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/12/02 19:49:16 INFO Executor: Fetching spark://192.168.122.1:35201/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with timestamp 1606967353351
20/12/02 19:49:16 INFO TransportClientFactory: Successfully created connection to /192.168.122.1:35201 after 28 ms (0 ms spent in bootstraps)
20/12/02 19:49:16 INFO Utils: Fetching spark://192.168.122.1:35201/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar to /tmp/spark-04d26462-dc3c-4144-b9c6-e758ef3d0ce6/userFiles-bc4e61a5-d6b4-4ff9-8a2b-0523239c4dc3/fetchFileTemp2670595056319393669.tmp
20/12/02 19:49:17 INFO Executor: Adding file:/tmp/spark-04d26462-dc3c-4144-b9c6-e758ef3d0ce6/userFiles-bc4e61a5-d6b4-4ff9-8a2b-0523239c4dc3/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar to class loader
20/12/02 19:49:17 INFO NewHadoopRDD: Input split: file:/tmp/adamTestyZdaqTT/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/12/02 19:49:17 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/12/02 19:49:17 INFO InternalParquetRecordReader: at row 0. reading next block
20/12/02 19:49:17 INFO CodecPool: Got brand-new decompressor [.gz]
20/12/02 19:49:17 INFO InternalParquetRecordReader: block read in memory in 42 ms. row count = 163064
20/12/02 19:49:20 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 1086 bytes result sent to driver
20/12/02 19:49:20 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3706 ms on 192.168.122.1 (executor driver) (1/1)
20/12/02 19:49:20 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/12/02 19:49:20 INFO DAGScheduler: ShuffleMapStage 0 (groupBy at SingleReadBucket.scala:97) finished in 3.829 s
20/12/02 19:49:20 INFO DAGScheduler: looking for newly runnable stages
20/12/02 19:49:20 INFO DAGScheduler: running: Set()
20/12/02 19:49:20 INFO DAGScheduler: waiting: Set(ResultStage 1)
20/12/02 19:49:20 INFO DAGScheduler: failed: Set()
20/12/02 19:49:20 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3805), which has no missing parents
20/12/02 19:49:20 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 90.1 KiB, free 408.5 MiB)
20/12/02 19:49:20 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 33.7 KiB, free 408.4 MiB)
20/12/02 19:49:20 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.122.1:40251 (size: 33.7 KiB, free: 408.8 MiB)
20/12/02 19:49:20 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1223
20/12/02 19:49:20 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3805) (first 15 tasks are for partitions Vector(0))
20/12/02 19:49:20 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
20/12/02 19:49:20 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, 192.168.122.1, executor driver, partition 0, NODE_LOCAL, 7143 bytes)
20/12/02 19:49:20 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
20/12/02 19:49:20 INFO ShuffleBlockFetcherIterator: Getting 1 (26.9 MiB) non-empty blocks including 1 (26.9 MiB) local and 0 (0.0 B) host-local and 0 (0.0 B) remote blocks
20/12/02 19:49:20 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 8 ms
20/12/02 19:49:22 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:49:22 INFO CodecConfig: Compression: GZIP
20/12/02 19:49:22 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:49:22 INFO ParquetOutputFormat: Parquet block size to 134217728
20/12/02 19:49:22 INFO ParquetOutputFormat: Parquet page size to 1048576
20/12/02 19:49:22 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/12/02 19:49:22 INFO ParquetOutputFormat: Dictionary is on
20/12/02 19:49:22 INFO ParquetOutputFormat: Validation is off
20/12/02 19:49:22 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/12/02 19:49:22 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/12/02 19:49:22 INFO ParquetOutputFormat: Page size checking is: estimated
20/12/02 19:49:22 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/12/02 19:49:22 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/12/02 19:49:22 INFO CodecPool: Got brand-new compressor [.gz]
20/12/02 19:49:23 INFO BlockManagerInfo: Removed broadcast_1_piece0 on 192.168.122.1:40251 in memory (size: 4.0 KiB, free: 408.8 MiB)
20/12/02 19:49:27 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 21417928
20/12/02 19:49:28 INFO FileOutputCommitter: Saved output of task 'attempt_20201202194916_0006_r_000000_0' to file:/tmp/adamTestyZdaqTT/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.fragments.adam/_temporary/0/task_20201202194916_0006_r_000000
20/12/02 19:49:28 INFO SparkHadoopMapRedUtil: attempt_20201202194916_0006_r_000000_0: Committed
20/12/02 19:49:28 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1365 bytes result sent to driver
20/12/02 19:49:28 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 7616 ms on 192.168.122.1 (executor driver) (1/1)
20/12/02 19:49:28 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
20/12/02 19:49:28 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 7.647 s
20/12/02 19:49:28 INFO DAGScheduler: Job 0 is finished. Cancelling potential speculative or zombie tasks for this job
20/12/02 19:49:28 INFO TaskSchedulerImpl: Killing all running tasks in stage 1: Stage finished
20/12/02 19:49:28 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 11.559858 s
20/12/02 19:49:28 INFO ParquetFileReader: Initiating action with parallelism: 5
20/12/02 19:49:28 INFO SparkHadoopWriter: Job job_20201202194916_0006 committed.
20/12/02 19:49:28 INFO SparkContext: Invoking stop() from shutdown hook
20/12/02 19:49:28 INFO SparkUI: Stopped Spark web UI at http://192.168.122.1:4040
20/12/02 19:49:28 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/12/02 19:49:28 INFO MemoryStore: MemoryStore cleared
20/12/02 19:49:28 INFO BlockManager: BlockManager stopped
20/12/02 19:49:28 INFO BlockManagerMaster: BlockManagerMaster stopped
20/12/02 19:49:28 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/12/02 19:49:28 INFO SparkContext: Successfully stopped SparkContext
20/12/02 19:49:28 INFO ShutdownHookManager: Shutdown hook called
20/12/02 19:49:28 INFO ShutdownHookManager: Deleting directory /tmp/spark-d57b3058-61bd-4fe4-b407-8d2ee97bacbf
20/12/02 19:49:28 INFO ShutdownHookManager: Deleting directory /tmp/spark-04d26462-dc3c-4144-b9c6-e758ef3d0ce6

# test that printing works
echo "Printing reads and fragments"
+ echo 'Printing reads and fragments'
Printing reads and fragments
${ADAM} print ${READS} 1>/dev/null 2>/dev/null
+ ./bin/adam-submit print mouse_chrM.bam.reads.adam
${ADAM} print ${FRAGMENTS} 1>/dev/null 2>/dev/null
+ ./bin/adam-submit print mouse_chrM.bam.fragments.adam

# run flagstat to verify that flagstat runs OK
echo "Printing read statistics"
+ echo 'Printing read statistics'
Printing read statistics
${ADAM} flagstat ${READS}
+ ./bin/adam-submit flagstat mouse_chrM.bam.reads.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/tmp/adamTestyZdaqTT/deleteMePleaseThisIsNoLongerNeeded/spark-3.0.1-bin-hadoop2.7/bin/spark-submit
20/12/02 19:49:46 WARN Utils: Your hostname, research-jenkins-worker-01 resolves to a loopback address: 127.0.1.1; using 192.168.122.1 instead (on interface virbr0)
20/12/02 19:49:46 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/12/02 19:49:47 WARN NativeCodeLoader: Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
log4j:WARN No appenders could be found for logger (org.bdgenomics.adam.cli.ADAMMain).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Using Spark's default log4j profile: org/apache/spark/log4j-defaults.properties
20/12/02 19:49:47 INFO SparkContext: Running Spark version 3.0.1
20/12/02 19:49:47 INFO ResourceUtils: ==============================================================
20/12/02 19:49:47 INFO ResourceUtils: Resources for spark.driver:

20/12/02 19:49:47 INFO ResourceUtils: ==============================================================
20/12/02 19:49:47 INFO SparkContext: Submitted application: flagstat
20/12/02 19:49:47 INFO SecurityManager: Changing view acls to: jenkins
20/12/02 19:49:47 INFO SecurityManager: Changing modify acls to: jenkins
20/12/02 19:49:47 INFO SecurityManager: Changing view acls groups to: 
20/12/02 19:49:47 INFO SecurityManager: Changing modify acls groups to: 
20/12/02 19:49:47 INFO SecurityManager: SecurityManager: authentication disabled; ui acls disabled; users  with view permissions: Set(jenkins); groups with view permissions: Set(); users  with modify permissions: Set(jenkins); groups with modify permissions: Set()
20/12/02 19:49:47 INFO Utils: Successfully started service 'sparkDriver' on port 33047.
20/12/02 19:49:48 INFO SparkEnv: Registering MapOutputTracker
20/12/02 19:49:48 INFO SparkEnv: Registering BlockManagerMaster
20/12/02 19:49:48 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/12/02 19:49:48 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/12/02 19:49:48 INFO SparkEnv: Registering BlockManagerMasterHeartbeat
20/12/02 19:49:48 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-1928c5ec-1587-4e8d-a625-fab81f89e6ea
20/12/02 19:49:48 INFO MemoryStore: MemoryStore started with capacity 408.9 MiB
20/12/02 19:49:48 INFO SparkEnv: Registering OutputCommitCoordinator
20/12/02 19:49:48 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/12/02 19:49:48 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.122.1:4040
20/12/02 19:49:48 INFO SparkContext: Added JAR file:/tmp/adamTestyZdaqTT/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar at spark://192.168.122.1:33047/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with timestamp 1606967388452
20/12/02 19:49:48 INFO Executor: Starting executor ID driver on host 192.168.122.1
20/12/02 19:49:48 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 40683.
20/12/02 19:49:48 INFO NettyBlockTransferService: Server created on 192.168.122.1:40683
20/12/02 19:49:48 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/12/02 19:49:48 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.122.1, 40683, None)
20/12/02 19:49:48 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.122.1:40683 with 408.9 MiB RAM, BlockManagerId(driver, 192.168.122.1, 40683, None)
20/12/02 19:49:48 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.122.1, 40683, None)
20/12/02 19:49:48 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.122.1, 40683, None)
20/12/02 19:49:49 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/12/02 19:49:49 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/12/02 19:49:49 INFO ADAMContext: Using the specified projection schema
20/12/02 19:49:49 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 320.5 KiB, free 408.6 MiB)
20/12/02 19:49:50 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 28.8 KiB, free 408.6 MiB)
20/12/02 19:49:50 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.122.1:40683 (size: 28.8 KiB, free: 408.9 MiB)
20/12/02 19:49:50 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1797
20/12/02 19:49:51 INFO FileInputFormat: Total input paths to process : 1
20/12/02 19:49:51 INFO ParquetInputFormat: Total input paths to process : 1
20/12/02 19:49:51 INFO SparkContext: Starting job: aggregate at FlagStat.scala:115
20/12/02 19:49:51 INFO DAGScheduler: Got job 0 (aggregate at FlagStat.scala:115) with 1 output partitions
20/12/02 19:49:51 INFO DAGScheduler: Final stage: ResultStage 0 (aggregate at FlagStat.scala:115)
20/12/02 19:49:51 INFO DAGScheduler: Parents of final stage: List()
20/12/02 19:49:51 INFO DAGScheduler: Missing parents: List()
20/12/02 19:49:51 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at FlagStat.scala:96), which has no missing parents
20/12/02 19:49:51 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.3 KiB, free 408.6 MiB)
20/12/02 19:49:51 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 2.9 KiB, free 408.6 MiB)
20/12/02 19:49:51 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.122.1:40683 (size: 2.9 KiB, free: 408.9 MiB)
20/12/02 19:49:51 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1223
20/12/02 19:49:51 INFO DAGScheduler: Submitting 1 missing tasks from ResultStage 0 (MapPartitionsRDD[2] at map at FlagStat.scala:96) (first 15 tasks are for partitions Vector(0))
20/12/02 19:49:51 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/12/02 19:49:51 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, 192.168.122.1, executor driver, partition 0, PROCESS_LOCAL, 7493 bytes)
20/12/02 19:49:51 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/12/02 19:49:51 INFO Executor: Fetching spark://192.168.122.1:33047/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar with timestamp 1606967388452
20/12/02 19:49:51 INFO TransportClientFactory: Successfully created connection to /192.168.122.1:33047 after 33 ms (0 ms spent in bootstraps)
20/12/02 19:49:51 INFO Utils: Fetching spark://192.168.122.1:33047/jars/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar to /tmp/spark-206c0d58-d66f-44d9-a759-eb0b50ad69a0/userFiles-0bb763c3-7734-416a-aa74-e7a8e5f4592c/fetchFileTemp2017627356377830522.tmp
20/12/02 19:49:52 INFO Executor: Adding file:/tmp/spark-206c0d58-d66f-44d9-a759-eb0b50ad69a0/userFiles-0bb763c3-7734-416a-aa74-e7a8e5f4592c/adam-assembly-spark3_2.12-0.33.0-SNAPSHOT.jar to class loader
20/12/02 19:49:52 INFO NewHadoopRDD: Input split: file:/tmp/adamTestyZdaqTT/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/12/02 19:49:52 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/12/02 19:49:52 INFO InternalParquetRecordReader: at row 0. reading next block
20/12/02 19:49:52 INFO CodecPool: Got brand-new decompressor [.gz]
20/12/02 19:49:52 INFO InternalParquetRecordReader: block read in memory in 20 ms. row count = 163064
20/12/02 19:49:53 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 988 bytes result sent to driver
20/12/02 19:49:53 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 1681 ms on 192.168.122.1 (executor driver) (1/1)
20/12/02 19:49:53 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/12/02 19:49:53 INFO DAGScheduler: ResultStage 0 (aggregate at FlagStat.scala:115) finished in 1.779 s
20/12/02 19:49:53 INFO DAGScheduler: Job 0 is finished. Cancelling potential speculative or zombie tasks for this job
20/12/02 19:49:53 INFO TaskSchedulerImpl: Killing all running tasks in stage 0: Stage finished
20/12/02 19:49:53 INFO DAGScheduler: Job 0 finished: aggregate at FlagStat.scala:115, took 1.831774 s
163064 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 primary duplicates
0 + 0 primary duplicates - both read and mate mapped
0 + 0 primary duplicates - only read mapped
0 + 0 primary duplicates - cross chromosome
0 + 0 secondary duplicates
0 + 0 secondary duplicates - both read and mate mapped
0 + 0 secondary duplicates - only read mapped
0 + 0 secondary duplicates - cross chromosome
160512 + 0 mapped (98.43%:0.00%)
163064 + 0 paired in sequencing
81524 + 0 read1
81540 + 0 read2
154982 + 0 properly paired (95.04%:0.00%)
158044 + 0 with itself and mate mapped
2468 + 0 singletons (1.51%:0.00%)
418 + 0 with mate mapped to a different chr
120 + 0 with mate mapped to a different chr (mapQ>=5)
20/12/02 19:49:53 INFO SparkContext: Invoking stop() from shutdown hook
20/12/02 19:49:53 INFO SparkUI: Stopped Spark web UI at http://192.168.122.1:4040
20/12/02 19:49:53 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/12/02 19:49:53 INFO MemoryStore: MemoryStore cleared
20/12/02 19:49:53 INFO BlockManager: BlockManager stopped
20/12/02 19:49:53 INFO BlockManagerMaster: BlockManagerMaster stopped
20/12/02 19:49:53 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/12/02 19:49:53 INFO SparkContext: Successfully stopped SparkContext
20/12/02 19:49:53 INFO ShutdownHookManager: Shutdown hook called
20/12/02 19:49:53 INFO ShutdownHookManager: Deleting directory /tmp/spark-206c0d58-d66f-44d9-a759-eb0b50ad69a0
20/12/02 19:49:53 INFO ShutdownHookManager: Deleting directory /tmp/spark-7aa90987-5ab9-48ab-8b70-001da034c87f
rm -rf ${ADAM_TMP_DIR}
+ rm -rf /tmp/adamTestyZdaqTT/deleteMePleaseThisIsNoLongerNeeded
popd
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu

pushd ${PROJECT_ROOT}
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu

# move back to Scala 2.12 as default
if [ ${SCALA_VERSION} == 2.11 ];
then
    set +e
    ./scripts/move_to_scala_2.12.sh
    set -e
fi
+ '[' 2.12 == 2.11 ']'
# move back to Spark 3.x as default
if [ ${SPARK_VERSION} == 2.4.7 ];
then
    set +e
    ./scripts/move_to_spark_3.sh
    set -e
fi
+ '[' 3.0.1 == 2.4.7 ']'

# test that the source is formatted correctly
./scripts/format-source
+ ./scripts/format-source
+++ dirname ./scripts/format-source
++ cd ./scripts
++ pwd
+ DIR=/home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu
+ mvn org.scalariform:scalariform-maven-plugin:format license:format
OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1g; support was removed in 8.0
[INFO] Scanning for projects...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Build Order:
[INFO] 
[INFO] ADAM_2.12                                                          [pom]
[INFO] ADAM_2.12: Shader workaround                                       [jar]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils                           [jar]
[INFO] ADAM_2.12: Core                                                    [jar]
[INFO] ADAM_2.12: APIs for Java, Python                                   [jar]
[INFO] ADAM_2.12: CLI                                                     [jar]
[INFO] ADAM_2.12: Assembly                                                [jar]
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[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-parent-spark3_2.12 >-------------
[INFO] Building ADAM_2.12 0.33.0-SNAPSHOT                                 [1/7]
[INFO] --------------------------------[ pom ]---------------------------------
[INFO] 
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[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-parent-spark3_2.12 ---
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Progress (5): 477 kB | 181/238 kB | 209 kB | 165/502 kB | 127/520 kB
                                                                    
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-container-default/1.0-beta-3.0.5/plexus-container-default-1.0-beta-3.0.5.jar (209 kB at 1.1 MB/s)
Progress (4): 477 kB | 181/238 kB | 165/502 kB | 131/520 kB
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Progress (4): 477 kB | 186/238 kB | 167/502 kB | 131/520 kB
                                                           
Downloading from central: https://repo.maven.apache.org/maven2/stax/stax-api/1.0.1/stax-api-1.0.1.jar
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Downloading from central: https://repo.maven.apache.org/maven2/org/sonatype/spice/model-builder/1.3/model-builder-1.3.jar
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-compat/3.0-alpha-2/maven-compat-3.0-alpha-2.jar (238 kB at 1.1 MB/s)
Progress (3): 244/502 kB | 287/520 kB | 82/169 kB
                                                 
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/2.0.5/plexus-utils-2.0.5.jar
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[INFO] Updating license headers...
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-shade-spark3_2.12 >-------------
[INFO] Building ADAM_2.12: Shader workaround 0.33.0-SNAPSHOT              [2/7]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-shade-spark3_2.12 ---
[INFO] Modified 0 of 0 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-shade-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] 
[INFO] ------------< org.bdgenomics.adam:adam-codegen-spark3_2.12 >------------
[INFO] Building ADAM_2.12: Avro-to-Dataset codegen utils 0.33.0-SNAPSHOT  [3/7]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-codegen-spark3_2.12 ---
[INFO] Modified 0 of 4 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-codegen-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-core-spark3_2.12 >--------------
[INFO] Building ADAM_2.12: Core 0.33.0-SNAPSHOT                           [4/7]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-core-spark3_2.12 ---
[INFO] Modified 0 of 204 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-core-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] 
[INFO] -------------< org.bdgenomics.adam:adam-apis-spark3_2.12 >--------------
[INFO] Building ADAM_2.12: APIs for Java, Python 0.33.0-SNAPSHOT          [5/7]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-apis-spark3_2.12 ---
[INFO] Modified 0 of 5 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-apis-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] 
[INFO] --------------< org.bdgenomics.adam:adam-cli-spark3_2.12 >--------------
[INFO] Building ADAM_2.12: CLI 0.33.0-SNAPSHOT                            [6/7]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-cli-spark3_2.12 ---
[INFO] Modified 0 of 29 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-cli-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] 
[INFO] -----------< org.bdgenomics.adam:adam-assembly-spark3_2.12 >------------
[INFO] Building ADAM_2.12: Assembly 0.33.0-SNAPSHOT                       [7/7]
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- scalariform-maven-plugin:0.1.4:format (default-cli) @ adam-assembly-spark3_2.12 ---
[INFO] Modified 0 of 1 .scala files
[INFO] 
[INFO] --- maven-license-plugin:1.10.b1:format (default-cli) @ adam-assembly-spark3_2.12 ---
[INFO] Updating license headers...
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for ADAM_2.12 0.33.0-SNAPSHOT:
[INFO] 
[INFO] ADAM_2.12 .......................................... SUCCESS [  8.958 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [  0.042 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [  0.096 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [  3.922 s]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [  0.142 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [  0.222 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [  0.022 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  14.913 s
[INFO] Finished at: 2020-12-02T19:50:09-08:00
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu
if test -n "$(git status --porcelain)"
then
    echo "Please run './scripts/format-source'"
    exit 1
fi
++ git status --porcelain
+ test -n ''
popd    
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.12/SPARK_VERSION/3.0.1/label/ubuntu

echo
+ echo

echo "All the tests passed"
+ echo 'All the tests passed'
All the tests passed
echo
+ echo

Recording test results
[Checks API] No suitable checks publisher found.
Publishing Scoverage XML and HTML report...
null
[Set GitHub commit status (universal)] SUCCESS on repos [] (sha:e6332ef) with context:ADAM-prb/HADOOP_VERSION=2.7.5,SCALA_VERSION=2.12,SPARK_VERSION=3.0.1,label=ubuntu
Finished: SUCCESS