Console Output

Skipping 2,162 KB.. Full Log
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary for ADAM_2.11 0.33.0-SNAPSHOT:
[INFO] 
[INFO] ADAM_2.11 .......................................... SUCCESS [  8.490 s]
[INFO] ADAM_2.11: Shader workaround ....................... SUCCESS [  1.270 s]
[INFO] ADAM_2.11: Avro-to-Dataset codegen utils ........... SUCCESS [  0.849 s]
[INFO] ADAM_2.11: Core .................................... SUCCESS [ 42.232 s]
[INFO] ADAM_2.11: APIs for Java, Python ................... SUCCESS [  2.602 s]
[INFO] ADAM_2.11: CLI ..................................... SUCCESS [  3.746 s]
[INFO] ADAM_2.11: Assembly ................................ SUCCESS [ 17.254 s]
[INFO] ADAM_2.11: R APIs .................................. SUCCESS [ 58.437 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  02:15 min
[INFO] Finished at: 2020-12-02T19:47:18-08:00
[INFO] ------------------------------------------------------------------------

# define filenames
BAM=mouse_chrM.bam
+ BAM=mouse_chrM.bam
READS=${BAM}.reads.adam
+ READS=mouse_chrM.bam.reads.adam
SORTED_READS=${BAM}.reads.sorted.adam
+ SORTED_READS=mouse_chrM.bam.reads.sorted.adam
FRAGMENTS=${BAM}.fragments.adam
+ FRAGMENTS=mouse_chrM.bam.fragments.adam
    
# fetch our input dataset
echo "Fetching BAM file"
+ echo 'Fetching BAM file'
Fetching BAM file
rm -rf ${BAM}
+ rm -rf mouse_chrM.bam
wget -q https://s3.amazonaws.com/bdgenomics-test/${BAM}
+ wget -q https://s3.amazonaws.com/bdgenomics-test/mouse_chrM.bam

# once fetched, convert BAM to ADAM
echo "Converting BAM to ADAM read format"
+ echo 'Converting BAM to ADAM read format'
Converting BAM to ADAM read format
rm -rf ${READS}
+ rm -rf mouse_chrM.bam.reads.adam
${ADAM} transformAlignments ${BAM} ${READS}
+ ./bin/adam-submit transformAlignments mouse_chrM.bam mouse_chrM.bam.reads.adam
Using ADAM_MAIN=org.bdgenomics.adam.cli.ADAMMain
Using spark-submit=/tmp/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7/bin/spark-submit
20/12/02 19:47:20 WARN Utils: Your hostname, research-jenkins-worker-06 resolves to a loopback address: 127.0.1.1; using 192.168.39.1 instead (on interface virbr1)
20/12/02 19:47:20 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/12/02 19:47:21 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 19:47:21 INFO SparkContext: Running Spark version 2.4.7
20/12/02 19:47:21 INFO SparkContext: Submitted application: transformAlignments
20/12/02 19:47:21 INFO SecurityManager: Changing view acls to: jenkins
20/12/02 19:47:21 INFO SecurityManager: Changing modify acls to: jenkins
20/12/02 19:47:21 INFO SecurityManager: Changing view acls groups to: 
20/12/02 19:47:21 INFO SecurityManager: Changing modify acls groups to: 
20/12/02 19:47:21 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 19:47:21 INFO Utils: Successfully started service 'sparkDriver' on port 41945.
20/12/02 19:47:22 INFO SparkEnv: Registering MapOutputTracker
20/12/02 19:47:22 INFO SparkEnv: Registering BlockManagerMaster
20/12/02 19:47:22 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/12/02 19:47:22 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/12/02 19:47:22 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-d8e20cce-1e3a-4545-ab79-f865cfaf8a81
20/12/02 19:47:22 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/12/02 19:47:22 INFO SparkEnv: Registering OutputCommitCoordinator
20/12/02 19:47:22 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/12/02 19:47:22 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.39.1:4040
20/12/02 19:47:22 INFO SparkContext: Added JAR file:/tmp/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar at spark://192.168.39.1:41945/jars/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar with timestamp 1606967242346
20/12/02 19:47:22 INFO Executor: Starting executor ID driver on host localhost
20/12/02 19:47:22 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 40383.
20/12/02 19:47:22 INFO NettyBlockTransferService: Server created on 192.168.39.1:40383
20/12/02 19:47:22 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/12/02 19:47:22 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.39.1, 40383, None)
20/12/02 19:47:22 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.39.1:40383 with 366.3 MB RAM, BlockManagerId(driver, 192.168.39.1, 40383, None)
20/12/02 19:47:22 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.39.1, 40383, None)
20/12/02 19:47:22 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.39.1, 40383, None)
20/12/02 19:47:22 INFO ADAMContext: Loading mouse_chrM.bam as BAM/CRAM/SAM and converting to Alignments.
20/12/02 19:47:23 INFO ADAMContext: Loaded header from file:/tmp/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam
20/12/02 19:47:23 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 284.3 KB, free 366.0 MB)
20/12/02 19:47:23 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 23.1 KB, free 366.0 MB)
20/12/02 19:47:23 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.39.1:40383 (size: 23.1 KB, free: 366.3 MB)
20/12/02 19:47:23 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:2053
20/12/02 19:47:24 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
20/12/02 19:47:24 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:47:24 INFO FileInputFormat: Total input paths to process : 1
20/12/02 19:47:25 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/12/02 19:47:25 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/12/02 19:47:25 INFO DAGScheduler: Final stage: ResultStage 0 (runJob at SparkHadoopWriter.scala:78)
20/12/02 19:47:25 INFO DAGScheduler: Parents of final stage: List()
20/12/02 19:47:25 INFO DAGScheduler: Missing parents: List()
20/12/02 19:47:25 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at GenomicDataset.scala:3805), which has no missing parents
20/12/02 19:47:25 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 82.1 KB, free 365.9 MB)
20/12/02 19:47:25 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 30.3 KB, free 365.9 MB)
20/12/02 19:47:25 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.39.1:40383 (size: 30.3 KB, free: 366.2 MB)
20/12/02 19:47:25 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1184
20/12/02 19:47:25 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 19:47:25 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/12/02 19:47:25 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 7962 bytes)
20/12/02 19:47:25 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/12/02 19:47:25 INFO Executor: Fetching spark://192.168.39.1:41945/jars/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar with timestamp 1606967242346
20/12/02 19:47:25 INFO TransportClientFactory: Successfully created connection to /192.168.39.1:41945 after 185 ms (0 ms spent in bootstraps)
20/12/02 19:47:25 INFO Utils: Fetching spark://192.168.39.1:41945/jars/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar to /tmp/spark-d8ea4c01-f22c-4467-a727-1da2e28a50fe/userFiles-7b84c78c-bb48-4148-8e84-f3339b98fc1e/fetchFileTemp476445964009552370.tmp
20/12/02 19:47:25 INFO Executor: Adding file:/tmp/spark-d8ea4c01-f22c-4467-a727-1da2e28a50fe/userFiles-7b84c78c-bb48-4148-8e84-f3339b98fc1e/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar to class loader
20/12/02 19:47:25 INFO NewHadoopRDD: Input split: file:/tmp/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam:83361792-833134657535
20/12/02 19:47:25 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:47:25 INFO CodecConfig: Compression: GZIP
20/12/02 19:47:25 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:47:25 INFO ParquetOutputFormat: Parquet block size to 134217728
20/12/02 19:47:25 INFO ParquetOutputFormat: Parquet page size to 1048576
20/12/02 19:47:25 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/12/02 19:47:25 INFO ParquetOutputFormat: Dictionary is on
20/12/02 19:47:25 INFO ParquetOutputFormat: Validation is off
20/12/02 19:47:25 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/12/02 19:47:25 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/12/02 19:47:25 INFO ParquetOutputFormat: Page size checking is: estimated
20/12/02 19:47:25 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/12/02 19:47:25 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/12/02 19:47:25 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 19:47:32 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16043959
20/12/02 19:47:32 INFO FileOutputCommitter: Saved output of task 'attempt_20201202194724_0002_r_000000_0' to file:/tmp/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/_temporary/0/task_20201202194724_0002_r_000000
20/12/02 19:47:32 INFO SparkHadoopMapRedUtil: attempt_20201202194724_0002_r_000000_0: Committed
20/12/02 19:47:32 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 893 bytes result sent to driver
20/12/02 19:47:32 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 7507 ms on localhost (executor driver) (1/1)
20/12/02 19:47:32 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/12/02 19:47:32 INFO DAGScheduler: ResultStage 0 (runJob at SparkHadoopWriter.scala:78) finished in 7.618 s
20/12/02 19:47:32 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 7.674858 s
20/12/02 19:47:32 INFO ParquetFileReader: Initiating action with parallelism: 5
20/12/02 19:47:32 INFO SparkHadoopWriter: Job job_20201202194724_0002 committed.
20/12/02 19:47:32 INFO SparkContext: Invoking stop() from shutdown hook
20/12/02 19:47:32 INFO SparkUI: Stopped Spark web UI at http://192.168.39.1:4040
20/12/02 19:47:32 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/12/02 19:47:32 INFO MemoryStore: MemoryStore cleared
20/12/02 19:47:32 INFO BlockManager: BlockManager stopped
20/12/02 19:47:32 INFO BlockManagerMaster: BlockManagerMaster stopped
20/12/02 19:47:32 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/12/02 19:47:32 INFO SparkContext: Successfully stopped SparkContext
20/12/02 19:47:32 INFO ShutdownHookManager: Shutdown hook called
20/12/02 19:47:32 INFO ShutdownHookManager: Deleting directory /tmp/spark-d8ea4c01-f22c-4467-a727-1da2e28a50fe
20/12/02 19:47:32 INFO ShutdownHookManager: Deleting directory /tmp/spark-9a981cb1-b61e-4851-8485-edd8c3b12b77

# 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/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7/bin/spark-submit
20/12/02 19:47:33 WARN Utils: Your hostname, research-jenkins-worker-06 resolves to a loopback address: 127.0.1.1; using 192.168.39.1 instead (on interface virbr1)
20/12/02 19:47:33 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/12/02 19:47:34 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 19:47:34 INFO SparkContext: Running Spark version 2.4.7
20/12/02 19:47:34 INFO SparkContext: Submitted application: transformAlignments
20/12/02 19:47:34 INFO SecurityManager: Changing view acls to: jenkins
20/12/02 19:47:34 INFO SecurityManager: Changing modify acls to: jenkins
20/12/02 19:47:34 INFO SecurityManager: Changing view acls groups to: 
20/12/02 19:47:34 INFO SecurityManager: Changing modify acls groups to: 
20/12/02 19:47:34 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 19:47:35 INFO Utils: Successfully started service 'sparkDriver' on port 33527.
20/12/02 19:47:35 INFO SparkEnv: Registering MapOutputTracker
20/12/02 19:47:35 INFO SparkEnv: Registering BlockManagerMaster
20/12/02 19:47:35 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/12/02 19:47:35 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/12/02 19:47:35 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-1fca2940-c519-4348-85a5-5ad482f924af
20/12/02 19:47:35 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/12/02 19:47:35 INFO SparkEnv: Registering OutputCommitCoordinator
20/12/02 19:47:35 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/12/02 19:47:35 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.39.1:4040
20/12/02 19:47:35 INFO SparkContext: Added JAR file:/tmp/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar at spark://192.168.39.1:33527/jars/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar with timestamp 1606967255423
20/12/02 19:47:35 INFO Executor: Starting executor ID driver on host localhost
20/12/02 19:47:35 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 46631.
20/12/02 19:47:35 INFO NettyBlockTransferService: Server created on 192.168.39.1:46631
20/12/02 19:47:35 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/12/02 19:47:35 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.39.1, 46631, None)
20/12/02 19:47:35 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.39.1:46631 with 366.3 MB RAM, BlockManagerId(driver, 192.168.39.1, 46631, None)
20/12/02 19:47:35 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.39.1, 46631, None)
20/12/02 19:47:35 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.39.1, 46631, None)
20/12/02 19:47:36 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/12/02 19:47:37 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/12/02 19:47:37 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 303.7 KB, free 366.0 MB)
20/12/02 19:47:38 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.4 KB, free 366.0 MB)
20/12/02 19:47:38 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.39.1:46631 (size: 27.4 KB, free: 366.3 MB)
20/12/02 19:47:38 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1792
20/12/02 19:47:38 INFO TransformAlignments: Sorting alignments by reference position, with references ordered by name
20/12/02 19:47:38 INFO RDDBoundAlignmentDataset: Sorting alignments by reference position
20/12/02 19:47:38 INFO FileInputFormat: Total input paths to process : 1
20/12/02 19:47:38 INFO ParquetInputFormat: Total input paths to process : 1
20/12/02 19:47:38 INFO RDDBoundAlignmentDataset: Saving data in ADAM format
20/12/02 19:47:38 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:47:38 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/12/02 19:47:38 INFO DAGScheduler: Registering RDD 2 (sortBy at AlignmentDataset.scala:1010) as input to shuffle 0
20/12/02 19:47:38 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/12/02 19:47:38 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
20/12/02 19:47:38 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
20/12/02 19:47:38 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
20/12/02 19:47:38 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at sortBy at AlignmentDataset.scala:1010), which has no missing parents
20/12/02 19:47:38 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.1 KB, free 366.0 MB)
20/12/02 19:47:38 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 3.0 KB, free 366.0 MB)
20/12/02 19:47:38 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.39.1:46631 (size: 3.0 KB, free: 366.3 MB)
20/12/02 19:47:38 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1184
20/12/02 19:47:38 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 19:47:38 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/12/02 19:47:38 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 8001 bytes)
20/12/02 19:47:38 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/12/02 19:47:38 INFO Executor: Fetching spark://192.168.39.1:33527/jars/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar with timestamp 1606967255423
20/12/02 19:47:38 INFO TransportClientFactory: Successfully created connection to /192.168.39.1:33527 after 37 ms (0 ms spent in bootstraps)
20/12/02 19:47:38 INFO Utils: Fetching spark://192.168.39.1:33527/jars/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar to /tmp/spark-7a923f7e-1a33-4a64-bc53-b9658355fb49/userFiles-f8efd1e0-1548-466a-90de-a74038a57043/fetchFileTemp4541034647215025881.tmp
20/12/02 19:47:39 INFO Executor: Adding file:/tmp/spark-7a923f7e-1a33-4a64-bc53-b9658355fb49/userFiles-f8efd1e0-1548-466a-90de-a74038a57043/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar to class loader
20/12/02 19:47:39 INFO NewHadoopRDD: Input split: file:/tmp/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/12/02 19:47:39 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/12/02 19:47:39 INFO InternalParquetRecordReader: at row 0. reading next block
20/12/02 19:47:39 INFO CodecPool: Got brand-new decompressor [.gz]
20/12/02 19:47:39 INFO InternalParquetRecordReader: block read in memory in 43 ms. row count = 163064
20/12/02 19:47:42 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 955 bytes result sent to driver
20/12/02 19:47:42 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3914 ms on localhost (executor driver) (1/1)
20/12/02 19:47:42 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/12/02 19:47:42 INFO DAGScheduler: ShuffleMapStage 0 (sortBy at AlignmentDataset.scala:1010) finished in 4.037 s
20/12/02 19:47:42 INFO DAGScheduler: looking for newly runnable stages
20/12/02 19:47:42 INFO DAGScheduler: running: Set()
20/12/02 19:47:42 INFO DAGScheduler: waiting: Set(ResultStage 1)
20/12/02 19:47:42 INFO DAGScheduler: failed: Set()
20/12/02 19:47:42 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[5] at map at GenomicDataset.scala:3805), which has no missing parents
20/12/02 19:47:42 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 83.4 KB, free 365.9 MB)
20/12/02 19:47:42 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 31.0 KB, free 365.9 MB)
20/12/02 19:47:42 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.39.1:46631 (size: 31.0 KB, free: 366.2 MB)
20/12/02 19:47:42 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1184
20/12/02 19:47:42 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 19:47:42 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
20/12/02 19:47:42 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 7662 bytes)
20/12/02 19:47:42 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
20/12/02 19:47:42 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks including 1 local blocks and 0 remote blocks
20/12/02 19:47:42 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 6 ms
20/12/02 19:47:44 INFO BlockManagerInfo: Removed broadcast_1_piece0 on 192.168.39.1:46631 in memory (size: 3.0 KB, free: 366.2 MB)
20/12/02 19:47:44 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:47:44 INFO CodecConfig: Compression: GZIP
20/12/02 19:47:44 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:47:44 INFO ParquetOutputFormat: Parquet block size to 134217728
20/12/02 19:47:44 INFO ParquetOutputFormat: Parquet page size to 1048576
20/12/02 19:47:44 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/12/02 19:47:44 INFO ParquetOutputFormat: Dictionary is on
20/12/02 19:47:44 INFO ParquetOutputFormat: Validation is off
20/12/02 19:47:44 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/12/02 19:47:44 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/12/02 19:47:44 INFO ParquetOutputFormat: Page size checking is: estimated
20/12/02 19:47:44 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/12/02 19:47:44 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/12/02 19:47:44 INFO CodecPool: Got brand-new compressor [.gz]
20/12/02 19:47:48 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 16004474
20/12/02 19:47:48 INFO FileOutputCommitter: Saved output of task 'attempt_20201202194738_0005_r_000000_0' to file:/tmp/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.sorted.adam/_temporary/0/task_20201202194738_0005_r_000000
20/12/02 19:47:48 INFO SparkHadoopMapRedUtil: attempt_20201202194738_0005_r_000000_0: Committed
20/12/02 19:47:48 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1237 bytes result sent to driver
20/12/02 19:47:48 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 6046 ms on localhost (executor driver) (1/1)
20/12/02 19:47:48 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
20/12/02 19:47:48 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 6.097 s
20/12/02 19:47:48 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 10.207020 s
20/12/02 19:47:48 INFO ParquetFileReader: Initiating action with parallelism: 5
20/12/02 19:47:48 INFO SparkHadoopWriter: Job job_20201202194738_0005 committed.
20/12/02 19:47:48 INFO SparkContext: Invoking stop() from shutdown hook
20/12/02 19:47:48 INFO SparkUI: Stopped Spark web UI at http://192.168.39.1:4040
20/12/02 19:47:48 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/12/02 19:47:48 INFO MemoryStore: MemoryStore cleared
20/12/02 19:47:48 INFO BlockManager: BlockManager stopped
20/12/02 19:47:48 INFO BlockManagerMaster: BlockManagerMaster stopped
20/12/02 19:47:48 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/12/02 19:47:48 INFO SparkContext: Successfully stopped SparkContext
20/12/02 19:47:48 INFO ShutdownHookManager: Shutdown hook called
20/12/02 19:47:48 INFO ShutdownHookManager: Deleting directory /tmp/spark-7a923f7e-1a33-4a64-bc53-b9658355fb49
20/12/02 19:47:48 INFO ShutdownHookManager: Deleting directory /tmp/spark-08637039-7fd2-4e44-af4e-2f29c55df7bb

# 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/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7/bin/spark-submit
20/12/02 19:47:49 WARN Utils: Your hostname, research-jenkins-worker-06 resolves to a loopback address: 127.0.1.1; using 192.168.39.1 instead (on interface virbr1)
20/12/02 19:47:49 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/12/02 19:47:50 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 19:47:50 INFO SparkContext: Running Spark version 2.4.7
20/12/02 19:47:50 INFO SparkContext: Submitted application: transformFragments
20/12/02 19:47:50 INFO SecurityManager: Changing view acls to: jenkins
20/12/02 19:47:50 INFO SecurityManager: Changing modify acls to: jenkins
20/12/02 19:47:50 INFO SecurityManager: Changing view acls groups to: 
20/12/02 19:47:50 INFO SecurityManager: Changing modify acls groups to: 
20/12/02 19:47:50 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 19:47:50 INFO Utils: Successfully started service 'sparkDriver' on port 40789.
20/12/02 19:47:50 INFO SparkEnv: Registering MapOutputTracker
20/12/02 19:47:50 INFO SparkEnv: Registering BlockManagerMaster
20/12/02 19:47:50 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/12/02 19:47:50 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/12/02 19:47:50 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-704054cb-89eb-4ed1-9aa5-69ebb1850984
20/12/02 19:47:50 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/12/02 19:47:50 INFO SparkEnv: Registering OutputCommitCoordinator
20/12/02 19:47:51 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/12/02 19:47:51 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.39.1:4040
20/12/02 19:47:51 INFO SparkContext: Added JAR file:/tmp/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar at spark://192.168.39.1:40789/jars/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar with timestamp 1606967271227
20/12/02 19:47:51 INFO Executor: Starting executor ID driver on host localhost
20/12/02 19:47:51 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 40225.
20/12/02 19:47:51 INFO NettyBlockTransferService: Server created on 192.168.39.1:40225
20/12/02 19:47:51 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/12/02 19:47:51 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.39.1, 40225, None)
20/12/02 19:47:51 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.39.1:40225 with 366.3 MB RAM, BlockManagerId(driver, 192.168.39.1, 40225, None)
20/12/02 19:47:51 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.39.1, 40225, None)
20/12/02 19:47:51 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.39.1, 40225, None)
20/12/02 19:47:51 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/12/02 19:47:53 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/12/02 19:47:53 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 303.7 KB, free 366.0 MB)
20/12/02 19:47:53 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 27.4 KB, free 366.0 MB)
20/12/02 19:47:53 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.39.1:40225 (size: 27.4 KB, free: 366.3 MB)
20/12/02 19:47:53 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1792
20/12/02 19:47:53 INFO FileInputFormat: Total input paths to process : 1
20/12/02 19:47:53 INFO ParquetInputFormat: Total input paths to process : 1
20/12/02 19:47:53 INFO RDDBoundFragmentDataset: Saving data in ADAM format
20/12/02 19:47:53 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:47:54 INFO SparkContext: Starting job: runJob at SparkHadoopWriter.scala:78
20/12/02 19:47:54 INFO DAGScheduler: Registering RDD 2 (groupBy at SingleReadBucket.scala:97) as input to shuffle 0
20/12/02 19:47:54 INFO DAGScheduler: Got job 0 (runJob at SparkHadoopWriter.scala:78) with 1 output partitions
20/12/02 19:47:54 INFO DAGScheduler: Final stage: ResultStage 1 (runJob at SparkHadoopWriter.scala:78)
20/12/02 19:47:54 INFO DAGScheduler: Parents of final stage: List(ShuffleMapStage 0)
20/12/02 19:47:54 INFO DAGScheduler: Missing parents: List(ShuffleMapStage 0)
20/12/02 19:47:54 INFO DAGScheduler: Submitting ShuffleMapStage 0 (MapPartitionsRDD[2] at groupBy at SingleReadBucket.scala:97), which has no missing parents
20/12/02 19:47:54 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 5.5 KB, free 366.0 MB)
20/12/02 19:47:54 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 3.1 KB, free 366.0 MB)
20/12/02 19:47:54 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.39.1:40225 (size: 3.1 KB, free: 366.3 MB)
20/12/02 19:47:54 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1184
20/12/02 19:47:54 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 19:47:54 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/12/02 19:47:54 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 8001 bytes)
20/12/02 19:47:54 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/12/02 19:47:54 INFO Executor: Fetching spark://192.168.39.1:40789/jars/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar with timestamp 1606967271227
20/12/02 19:47:54 INFO TransportClientFactory: Successfully created connection to /192.168.39.1:40789 after 40 ms (0 ms spent in bootstraps)
20/12/02 19:47:54 INFO Utils: Fetching spark://192.168.39.1:40789/jars/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar to /tmp/spark-0ea02968-915b-4b85-a4b1-967b89d025ac/userFiles-bd09c1a1-4a92-4ad9-9c25-f3c1fa96656c/fetchFileTemp720249239356289204.tmp
20/12/02 19:47:54 INFO Executor: Adding file:/tmp/spark-0ea02968-915b-4b85-a4b1-967b89d025ac/userFiles-bd09c1a1-4a92-4ad9-9c25-f3c1fa96656c/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar to class loader
20/12/02 19:47:54 INFO NewHadoopRDD: Input split: file:/tmp/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/12/02 19:47:55 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/12/02 19:47:55 INFO InternalParquetRecordReader: at row 0. reading next block
20/12/02 19:47:55 INFO CodecPool: Got brand-new decompressor [.gz]
20/12/02 19:47:55 INFO InternalParquetRecordReader: block read in memory in 46 ms. row count = 163064
20/12/02 19:47:57 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 955 bytes result sent to driver
20/12/02 19:47:58 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 3861 ms on localhost (executor driver) (1/1)
20/12/02 19:47:58 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/12/02 19:47:58 INFO DAGScheduler: ShuffleMapStage 0 (groupBy at SingleReadBucket.scala:97) finished in 3.956 s
20/12/02 19:47:58 INFO DAGScheduler: looking for newly runnable stages
20/12/02 19:47:58 INFO DAGScheduler: running: Set()
20/12/02 19:47:58 INFO DAGScheduler: waiting: Set(ResultStage 1)
20/12/02 19:47:58 INFO DAGScheduler: failed: Set()
20/12/02 19:47:58 INFO DAGScheduler: Submitting ResultStage 1 (MapPartitionsRDD[6] at map at GenomicDataset.scala:3805), which has no missing parents
20/12/02 19:47:58 INFO MemoryStore: Block broadcast_2 stored as values in memory (estimated size 86.3 KB, free 365.9 MB)
20/12/02 19:47:58 INFO MemoryStore: Block broadcast_2_piece0 stored as bytes in memory (estimated size 32.3 KB, free 365.9 MB)
20/12/02 19:47:58 INFO BlockManagerInfo: Added broadcast_2_piece0 in memory on 192.168.39.1:40225 (size: 32.3 KB, free: 366.2 MB)
20/12/02 19:47:58 INFO SparkContext: Created broadcast 2 from broadcast at DAGScheduler.scala:1184
20/12/02 19:47:58 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 19:47:58 INFO TaskSchedulerImpl: Adding task set 1.0 with 1 tasks
20/12/02 19:47:58 INFO TaskSetManager: Starting task 0.0 in stage 1.0 (TID 1, localhost, executor driver, partition 0, ANY, 7662 bytes)
20/12/02 19:47:58 INFO Executor: Running task 0.0 in stage 1.0 (TID 1)
20/12/02 19:47:58 INFO ShuffleBlockFetcherIterator: Getting 1 non-empty blocks including 1 local blocks and 0 remote blocks
20/12/02 19:47:58 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 6 ms
20/12/02 19:47:59 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:47:59 INFO CodecConfig: Compression: GZIP
20/12/02 19:47:59 INFO FileOutputCommitter: File Output Committer Algorithm version is 1
20/12/02 19:47:59 INFO ParquetOutputFormat: Parquet block size to 134217728
20/12/02 19:47:59 INFO ParquetOutputFormat: Parquet page size to 1048576
20/12/02 19:47:59 INFO ParquetOutputFormat: Parquet dictionary page size to 1048576
20/12/02 19:47:59 INFO ParquetOutputFormat: Dictionary is on
20/12/02 19:47:59 INFO ParquetOutputFormat: Validation is off
20/12/02 19:47:59 INFO ParquetOutputFormat: Writer version is: PARQUET_1_0
20/12/02 19:47:59 INFO ParquetOutputFormat: Maximum row group padding size is 8388608 bytes
20/12/02 19:47:59 INFO ParquetOutputFormat: Page size checking is: estimated
20/12/02 19:47:59 INFO ParquetOutputFormat: Min row count for page size check is: 100
20/12/02 19:47:59 INFO ParquetOutputFormat: Max row count for page size check is: 10000
20/12/02 19:47:59 INFO CodecPool: Got brand-new compressor [.gz]
20/12/02 19:48:04 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 21417928
20/12/02 19:48:05 INFO FileOutputCommitter: Saved output of task 'attempt_20201202194753_0006_r_000000_0' to file:/tmp/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.fragments.adam/_temporary/0/task_20201202194753_0006_r_000000
20/12/02 19:48:05 INFO SparkHadoopMapRedUtil: attempt_20201202194753_0006_r_000000_0: Committed
20/12/02 19:48:05 INFO Executor: Finished task 0.0 in stage 1.0 (TID 1). 1280 bytes result sent to driver
20/12/02 19:48:05 INFO TaskSetManager: Finished task 0.0 in stage 1.0 (TID 1) in 7061 ms on localhost (executor driver) (1/1)
20/12/02 19:48:05 INFO TaskSchedulerImpl: Removed TaskSet 1.0, whose tasks have all completed, from pool 
20/12/02 19:48:05 INFO DAGScheduler: ResultStage 1 (runJob at SparkHadoopWriter.scala:78) finished in 7.103 s
20/12/02 19:48:05 INFO DAGScheduler: Job 0 finished: runJob at SparkHadoopWriter.scala:78, took 11.133442 s
20/12/02 19:48:05 INFO ParquetFileReader: Initiating action with parallelism: 5
20/12/02 19:48:05 INFO SparkHadoopWriter: Job job_20201202194753_0006 committed.
20/12/02 19:48:05 INFO SparkContext: Invoking stop() from shutdown hook
20/12/02 19:48:05 INFO SparkUI: Stopped Spark web UI at http://192.168.39.1:4040
20/12/02 19:48:05 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/12/02 19:48:05 INFO MemoryStore: MemoryStore cleared
20/12/02 19:48:05 INFO BlockManager: BlockManager stopped
20/12/02 19:48:05 INFO BlockManagerMaster: BlockManagerMaster stopped
20/12/02 19:48:05 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/12/02 19:48:05 INFO SparkContext: Successfully stopped SparkContext
20/12/02 19:48:05 INFO ShutdownHookManager: Shutdown hook called
20/12/02 19:48:05 INFO ShutdownHookManager: Deleting directory /tmp/spark-3309cc1a-05ed-4bf0-98a9-524237c0dc02
20/12/02 19:48:05 INFO ShutdownHookManager: Deleting directory /tmp/spark-0ea02968-915b-4b85-a4b1-967b89d025ac

# 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/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.7-bin-hadoop2.7/bin/spark-submit
20/12/02 19:48:22 WARN Utils: Your hostname, research-jenkins-worker-06 resolves to a loopback address: 127.0.1.1; using 192.168.39.1 instead (on interface virbr1)
20/12/02 19:48:22 WARN Utils: Set SPARK_LOCAL_IP if you need to bind to another address
20/12/02 19:48:23 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 19:48:23 INFO SparkContext: Running Spark version 2.4.7
20/12/02 19:48:23 INFO SparkContext: Submitted application: flagstat
20/12/02 19:48:23 INFO SecurityManager: Changing view acls to: jenkins
20/12/02 19:48:23 INFO SecurityManager: Changing modify acls to: jenkins
20/12/02 19:48:23 INFO SecurityManager: Changing view acls groups to: 
20/12/02 19:48:23 INFO SecurityManager: Changing modify acls groups to: 
20/12/02 19:48:23 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 19:48:23 INFO Utils: Successfully started service 'sparkDriver' on port 33859.
20/12/02 19:48:23 INFO SparkEnv: Registering MapOutputTracker
20/12/02 19:48:23 INFO SparkEnv: Registering BlockManagerMaster
20/12/02 19:48:23 INFO BlockManagerMasterEndpoint: Using org.apache.spark.storage.DefaultTopologyMapper for getting topology information
20/12/02 19:48:23 INFO BlockManagerMasterEndpoint: BlockManagerMasterEndpoint up
20/12/02 19:48:23 INFO DiskBlockManager: Created local directory at /tmp/blockmgr-094b2ba3-0eae-497e-8a36-51f17ef6ffbb
20/12/02 19:48:23 INFO MemoryStore: MemoryStore started with capacity 366.3 MB
20/12/02 19:48:23 INFO SparkEnv: Registering OutputCommitCoordinator
20/12/02 19:48:23 INFO Utils: Successfully started service 'SparkUI' on port 4040.
20/12/02 19:48:24 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.39.1:4040
20/12/02 19:48:24 INFO SparkContext: Added JAR file:/tmp/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded/adam-assembly/target/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar at spark://192.168.39.1:33859/jars/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar with timestamp 1606967304075
20/12/02 19:48:24 INFO Executor: Starting executor ID driver on host localhost
20/12/02 19:48:24 INFO Utils: Successfully started service 'org.apache.spark.network.netty.NettyBlockTransferService' on port 45877.
20/12/02 19:48:24 INFO NettyBlockTransferService: Server created on 192.168.39.1:45877
20/12/02 19:48:24 INFO BlockManager: Using org.apache.spark.storage.RandomBlockReplicationPolicy for block replication policy
20/12/02 19:48:24 INFO BlockManagerMaster: Registering BlockManager BlockManagerId(driver, 192.168.39.1, 45877, None)
20/12/02 19:48:24 INFO BlockManagerMasterEndpoint: Registering block manager 192.168.39.1:45877 with 366.3 MB RAM, BlockManagerId(driver, 192.168.39.1, 45877, None)
20/12/02 19:48:24 INFO BlockManagerMaster: Registered BlockManager BlockManagerId(driver, 192.168.39.1, 45877, None)
20/12/02 19:48:24 INFO BlockManager: Initialized BlockManager: BlockManagerId(driver, 192.168.39.1, 45877, None)
20/12/02 19:48:24 INFO ADAMContext: Loading mouse_chrM.bam.reads.adam as Parquet of Alignments.
20/12/02 19:48:24 INFO ADAMContext: Reading the ADAM file at mouse_chrM.bam.reads.adam to create RDD
20/12/02 19:48:24 INFO ADAMContext: Using the specified projection schema
20/12/02 19:48:25 INFO MemoryStore: Block broadcast_0 stored as values in memory (estimated size 313.1 KB, free 366.0 MB)
20/12/02 19:48:25 INFO MemoryStore: Block broadcast_0_piece0 stored as bytes in memory (estimated size 28.4 KB, free 366.0 MB)
20/12/02 19:48:25 INFO BlockManagerInfo: Added broadcast_0_piece0 in memory on 192.168.39.1:45877 (size: 28.4 KB, free: 366.3 MB)
20/12/02 19:48:25 INFO SparkContext: Created broadcast 0 from newAPIHadoopFile at ADAMContext.scala:1792
20/12/02 19:48:26 INFO FileInputFormat: Total input paths to process : 1
20/12/02 19:48:26 INFO ParquetInputFormat: Total input paths to process : 1
20/12/02 19:48:26 INFO SparkContext: Starting job: aggregate at FlagStat.scala:115
20/12/02 19:48:26 INFO DAGScheduler: Got job 0 (aggregate at FlagStat.scala:115) with 1 output partitions
20/12/02 19:48:26 INFO DAGScheduler: Final stage: ResultStage 0 (aggregate at FlagStat.scala:115)
20/12/02 19:48:26 INFO DAGScheduler: Parents of final stage: List()
20/12/02 19:48:26 INFO DAGScheduler: Missing parents: List()
20/12/02 19:48:26 INFO DAGScheduler: Submitting ResultStage 0 (MapPartitionsRDD[2] at map at FlagStat.scala:96), which has no missing parents
20/12/02 19:48:26 INFO MemoryStore: Block broadcast_1 stored as values in memory (estimated size 4.3 KB, free 366.0 MB)
20/12/02 19:48:26 INFO MemoryStore: Block broadcast_1_piece0 stored as bytes in memory (estimated size 2.5 KB, free 366.0 MB)
20/12/02 19:48:26 INFO BlockManagerInfo: Added broadcast_1_piece0 in memory on 192.168.39.1:45877 (size: 2.5 KB, free: 366.3 MB)
20/12/02 19:48:26 INFO SparkContext: Created broadcast 1 from broadcast at DAGScheduler.scala:1184
20/12/02 19:48:26 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 19:48:26 INFO TaskSchedulerImpl: Adding task set 0.0 with 1 tasks
20/12/02 19:48:26 INFO TaskSetManager: Starting task 0.0 in stage 0.0 (TID 0, localhost, executor driver, partition 0, PROCESS_LOCAL, 8012 bytes)
20/12/02 19:48:26 INFO Executor: Running task 0.0 in stage 0.0 (TID 0)
20/12/02 19:48:27 INFO Executor: Fetching spark://192.168.39.1:33859/jars/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar with timestamp 1606967304075
20/12/02 19:48:27 INFO TransportClientFactory: Successfully created connection to /192.168.39.1:33859 after 40 ms (0 ms spent in bootstraps)
20/12/02 19:48:27 INFO Utils: Fetching spark://192.168.39.1:33859/jars/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar to /tmp/spark-3db3b9e4-86b2-46fe-8b97-90e9f51c8104/userFiles-c77ec483-0193-4b66-bd10-05d04d5e578b/fetchFileTemp4816999047774836785.tmp
20/12/02 19:48:27 INFO Executor: Adding file:/tmp/spark-3db3b9e4-86b2-46fe-8b97-90e9f51c8104/userFiles-c77ec483-0193-4b66-bd10-05d04d5e578b/adam-assembly-spark2_2.11-0.33.0-SNAPSHOT.jar to class loader
20/12/02 19:48:27 INFO NewHadoopRDD: Input split: file:/tmp/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded/mouse_chrM.bam.reads.adam/part-r-00000.gz.parquet:0+10132211
20/12/02 19:48:27 INFO InternalParquetRecordReader: RecordReader initialized will read a total of 163064 records.
20/12/02 19:48:27 INFO InternalParquetRecordReader: at row 0. reading next block
20/12/02 19:48:27 INFO CodecPool: Got brand-new decompressor [.gz]
20/12/02 19:48:27 INFO InternalParquetRecordReader: block read in memory in 25 ms. row count = 163064
20/12/02 19:48:28 INFO Executor: Finished task 0.0 in stage 0.0 (TID 0). 859 bytes result sent to driver
20/12/02 19:48:28 INFO TaskSetManager: Finished task 0.0 in stage 0.0 (TID 0) in 1775 ms on localhost (executor driver) (1/1)
20/12/02 19:48:28 INFO TaskSchedulerImpl: Removed TaskSet 0.0, whose tasks have all completed, from pool 
20/12/02 19:48:28 INFO DAGScheduler: ResultStage 0 (aggregate at FlagStat.scala:115) finished in 1.859 s
20/12/02 19:48:28 INFO DAGScheduler: Job 0 finished: aggregate at FlagStat.scala:115, took 1.913923 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 19:48:28 INFO SparkContext: Invoking stop() from shutdown hook
20/12/02 19:48:28 INFO SparkUI: Stopped Spark web UI at http://192.168.39.1:4040
20/12/02 19:48:28 INFO MapOutputTrackerMasterEndpoint: MapOutputTrackerMasterEndpoint stopped!
20/12/02 19:48:28 INFO MemoryStore: MemoryStore cleared
20/12/02 19:48:28 INFO BlockManager: BlockManager stopped
20/12/02 19:48:28 INFO BlockManagerMaster: BlockManagerMaster stopped
20/12/02 19:48:28 INFO OutputCommitCoordinator$OutputCommitCoordinatorEndpoint: OutputCommitCoordinator stopped!
20/12/02 19:48:28 INFO SparkContext: Successfully stopped SparkContext
20/12/02 19:48:28 INFO ShutdownHookManager: Shutdown hook called
20/12/02 19:48:28 INFO ShutdownHookManager: Deleting directory /tmp/spark-518f20f7-4380-4f92-9f5d-4e43628ae973
20/12/02 19:48:28 INFO ShutdownHookManager: Deleting directory /tmp/spark-3db3b9e4-86b2-46fe-8b97-90e9f51c8104
rm -rf ${ADAM_TMP_DIR}
+ rm -rf /tmp/adamTesteRddlfB/deleteMePleaseThisIsNoLongerNeeded
popd
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu

pushd ${PROJECT_ROOT}
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/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
+ '[' 2.11 == 2.11 ']'
+ set +e
+ ./scripts/move_to_scala_2.12.sh
+ set -e
# 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
+ '[' 2.4.7 == 2.4.7 ']'
+ set +e
+ ./scripts/move_to_spark_3.sh
+ set -e

# 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/2.11/SPARK_VERSION/2.4.7/label/ubuntu/scripts
+ pushd /home/jenkins/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu/scripts/..
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/label/ubuntu ~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/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 (4): 154/238 kB | 85/209 kB | 53/502 kB | 49/520 kB
Progress (4): 154/238 kB | 88/209 kB | 53/502 kB | 49/520 kB
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Progress (4): 156/238 kB | 90/209 kB | 57/502 kB | 53/520 kB
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Progress (4): 156/238 kB | 93/209 kB | 57/502 kB | 57/520 kB
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Progress (4): 159/238 kB | 96/209 kB | 57/502 kB | 57/520 kB
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Progress (4): 162/238 kB | 99/209 kB | 57/502 kB | 57/520 kB
Progress (5): 162/238 kB | 99/209 kB | 57/502 kB | 57/520 kB | 4.1/36 kB
Progress (5): 162/238 kB | 99/209 kB | 57/502 kB | 61/520 kB | 4.1/36 kB
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Progress (5): 162/238 kB | 99/209 kB | 61/502 kB | 66/520 kB | 8.2/36 kB
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Progress (5): 165/238 kB | 104/209 kB | 61/502 kB | 66/520 kB | 12/36 kB 
Progress (5): 165/238 kB | 104/209 kB | 61/502 kB | 70/520 kB | 12/36 kB
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Progress (5): 165/238 kB | 104/209 kB | 66/502 kB | 74/520 kB | 12/36 kB
Progress (5): 165/238 kB | 104/209 kB | 66/502 kB | 74/520 kB | 16/36 kB
Progress (5): 165/238 kB | 107/209 kB | 66/502 kB | 74/520 kB | 16/36 kB
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Progress (5): 167/238 kB | 110/209 kB | 66/502 kB | 74/520 kB | 16/36 kB
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Progress (5): 167/238 kB | 110/209 kB | 66/502 kB | 78/520 kB | 20/36 kB
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Progress (5): 170/238 kB | 115/209 kB | 70/502 kB | 86/520 kB | 25/36 kB
Progress (5): 170/238 kB | 118/209 kB | 70/502 kB | 86/520 kB | 25/36 kB
Progress (5): 170/238 kB | 118/209 kB | 70/502 kB | 86/520 kB | 29/36 kB
Progress (5): 170/238 kB | 118/209 kB | 74/502 kB | 86/520 kB | 29/36 kB
Progress (5): 170/238 kB | 118/209 kB | 74/502 kB | 86/520 kB | 33/36 kB
Progress (5): 170/238 kB | 121/209 kB | 74/502 kB | 86/520 kB | 33/36 kB
Progress (5): 170/238 kB | 121/209 kB | 74/502 kB | 90/520 kB | 33/36 kB
Progress (5): 173/238 kB | 121/209 kB | 74/502 kB | 90/520 kB | 33/36 kB
Progress (5): 173/238 kB | 121/209 kB | 74/502 kB | 94/520 kB | 33/36 kB
Progress (5): 173/238 kB | 123/209 kB | 74/502 kB | 94/520 kB | 33/36 kB
Progress (5): 173/238 kB | 123/209 kB | 74/502 kB | 94/520 kB | 36 kB   
Progress (5): 173/238 kB | 123/209 kB | 78/502 kB | 94/520 kB | 36 kB
Progress (5): 173/238 kB | 126/209 kB | 78/502 kB | 94/520 kB | 36 kB
Progress (5): 173/238 kB | 126/209 kB | 78/502 kB | 98/520 kB | 36 kB
Progress (5): 175/238 kB | 126/209 kB | 78/502 kB | 98/520 kB | 36 kB
Progress (5): 175/238 kB | 129/209 kB | 78/502 kB | 98/520 kB | 36 kB
Progress (5): 175/238 kB | 129/209 kB | 82/502 kB | 98/520 kB | 36 kB
Progress (5): 175/238 kB | 132/209 kB | 82/502 kB | 98/520 kB | 36 kB
Progress (5): 178/238 kB | 132/209 kB | 82/502 kB | 98/520 kB | 36 kB
Progress (5): 178/238 kB | 132/209 kB | 82/502 kB | 102/520 kB | 36 kB
Progress (5): 181/238 kB | 132/209 kB | 82/502 kB | 102/520 kB | 36 kB
Progress (5): 181/238 kB | 134/209 kB | 82/502 kB | 102/520 kB | 36 kB
Progress (5): 181/238 kB | 134/209 kB | 86/502 kB | 102/520 kB | 36 kB
Progress (5): 181/238 kB | 137/209 kB | 86/502 kB | 102/520 kB | 36 kB
Progress (5): 184/238 kB | 137/209 kB | 86/502 kB | 102/520 kB | 36 kB
Progress (5): 184/238 kB | 140/209 kB | 86/502 kB | 102/520 kB | 36 kB
Progress (5): 184/238 kB | 140/209 kB | 86/502 kB | 106/520 kB | 36 kB
Progress (5): 186/238 kB | 140/209 kB | 86/502 kB | 106/520 kB | 36 kB
Progress (5): 186/238 kB | 140/209 kB | 90/502 kB | 106/520 kB | 36 kB
Progress (5): 189/238 kB | 140/209 kB | 90/502 kB | 106/520 kB | 36 kB
Progress (5): 189/238 kB | 140/209 kB | 90/502 kB | 111/520 kB | 36 kB
Progress (5): 189/238 kB | 143/209 kB | 90/502 kB | 111/520 kB | 36 kB
Progress (5): 189/238 kB | 143/209 kB | 90/502 kB | 115/520 kB | 36 kB
Progress (5): 192/238 kB | 143/209 kB | 90/502 kB | 115/520 kB | 36 kB
Progress (5): 192/238 kB | 143/209 kB | 94/502 kB | 115/520 kB | 36 kB
Progress (5): 195/238 kB | 143/209 kB | 94/502 kB | 115/520 kB | 36 kB
Progress (5): 195/238 kB | 143/209 kB | 94/502 kB | 119/520 kB | 36 kB
Progress (5): 195/238 kB | 145/209 kB | 94/502 kB | 119/520 kB | 36 kB
Progress (5): 195/238 kB | 145/209 kB | 94/502 kB | 123/520 kB | 36 kB
Progress (5): 197/238 kB | 145/209 kB | 94/502 kB | 123/520 kB | 36 kB
Progress (5): 197/238 kB | 145/209 kB | 98/502 kB | 123/520 kB | 36 kB
Progress (5): 200/238 kB | 145/209 kB | 98/502 kB | 123/520 kB | 36 kB
Progress (5): 200/238 kB | 145/209 kB | 98/502 kB | 127/520 kB | 36 kB
Progress (5): 200/238 kB | 148/209 kB | 98/502 kB | 127/520 kB | 36 kB
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Progress (5): 200/238 kB | 148/209 kB | 102/502 kB | 131/520 kB | 36 kB
Progress (5): 203/238 kB | 148/209 kB | 102/502 kB | 131/520 kB | 36 kB
Progress (5): 203/238 kB | 148/209 kB | 106/502 kB | 131/520 kB | 36 kB
Progress (5): 203/238 kB | 148/209 kB | 106/502 kB | 135/520 kB | 36 kB
Progress (5): 203/238 kB | 151/209 kB | 106/502 kB | 135/520 kB | 36 kB
Progress (5): 203/238 kB | 151/209 kB | 106/502 kB | 139/520 kB | 36 kB
Progress (5): 203/238 kB | 151/209 kB | 111/502 kB | 139/520 kB | 36 kB
Progress (5): 206/238 kB | 151/209 kB | 111/502 kB | 139/520 kB | 36 kB
                                                                       
Downloaded from central: https://repo.maven.apache.org/maven2/org/sonatype/spice/model-builder/1.3/model-builder-1.3.jar (36 kB at 204 kB/s)
Progress (4): 206/238 kB | 151/209 kB | 115/502 kB | 139/520 kB
Progress (4): 206/238 kB | 151/209 kB | 115/502 kB | 143/520 kB
Progress (4): 206/238 kB | 154/209 kB | 115/502 kB | 143/520 kB
Progress (4): 206/238 kB | 154/209 kB | 119/502 kB | 143/520 kB
Progress (4): 206/238 kB | 154/209 kB | 119/502 kB | 147/520 kB
                                                               
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-project-builder/3.0-alpha-2/maven-project-builder-3.0-alpha-2.jar
Progress (4): 208/238 kB | 154/209 kB | 119/502 kB | 147/520 kB
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Progress (4): 208/238 kB | 156/209 kB | 123/502 kB | 152/520 kB
Progress (4): 208/238 kB | 156/209 kB | 127/502 kB | 152/520 kB
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Progress (5): 225/238 kB | 175/209 kB | 147/502 kB | 180/520 kB | 4.1/169 kB
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Progress (5): 230/238 kB | 184/209 kB | 152/502 kB | 188/520 kB | 8.2/169 kB
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Progress (5): 236/238 kB | 189/209 kB | 156/502 kB | 197/520 kB | 12/169 kB 
Progress (5): 236/238 kB | 192/209 kB | 156/502 kB | 197/520 kB | 12/169 kB
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Progress (5): 238 kB | 192/209 kB | 160/502 kB | 197/520 kB | 12/169 kB
Progress (5): 238 kB | 195/209 kB | 160/502 kB | 197/520 kB | 12/169 kB
Progress (5): 238 kB | 195/209 kB | 160/502 kB | 197/520 kB | 16/169 kB
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Progress (5): 238 kB | 200/209 kB | 164/502 kB | 201/520 kB | 16/169 kB
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Progress (5): 238 kB | 200/209 kB | 164/502 kB | 205/520 kB | 20/169 kB
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Progress (5): 238 kB | 203/209 kB | 164/502 kB | 209/520 kB | 20/169 kB
Progress (5): 238 kB | 203/209 kB | 168/502 kB | 209/520 kB | 20/169 kB
Progress (5): 238 kB | 203/209 kB | 168/502 kB | 213/520 kB | 20/169 kB
Progress (5): 238 kB | 203/209 kB | 168/502 kB | 213/520 kB | 25/169 kB
Progress (5): 238 kB | 203/209 kB | 172/502 kB | 213/520 kB | 25/169 kB
Progress (5): 238 kB | 206/209 kB | 172/502 kB | 213/520 kB | 25/169 kB
Progress (5): 238 kB | 206/209 kB | 176/502 kB | 213/520 kB | 25/169 kB
Progress (5): 238 kB | 208/209 kB | 176/502 kB | 213/520 kB | 25/169 kB
Progress (5): 238 kB | 208/209 kB | 176/502 kB | 213/520 kB | 29/169 kB
Progress (5): 238 kB | 208/209 kB | 176/502 kB | 217/520 kB | 29/169 kB
Progress (5): 238 kB | 208/209 kB | 176/502 kB | 217/520 kB | 33/169 kB
Progress (5): 238 kB | 209 kB | 176/502 kB | 217/520 kB | 33/169 kB    
Progress (5): 238 kB | 209 kB | 180/502 kB | 217/520 kB | 33/169 kB
Progress (5): 238 kB | 209 kB | 180/502 kB | 217/520 kB | 37/169 kB
Progress (5): 238 kB | 209 kB | 180/502 kB | 221/520 kB | 37/169 kB
Progress (5): 238 kB | 209 kB | 180/502 kB | 221/520 kB | 41/169 kB
Progress (5): 238 kB | 209 kB | 184/502 kB | 221/520 kB | 41/169 kB
Progress (5): 238 kB | 209 kB | 184/502 kB | 221/520 kB | 45/169 kB
Progress (5): 238 kB | 209 kB | 184/502 kB | 225/520 kB | 45/169 kB
Progress (5): 238 kB | 209 kB | 184/502 kB | 225/520 kB | 49/169 kB
Progress (5): 238 kB | 209 kB | 188/502 kB | 225/520 kB | 49/169 kB
Progress (5): 238 kB | 209 kB | 188/502 kB | 229/520 kB | 49/169 kB
Progress (5): 238 kB | 209 kB | 188/502 kB | 229/520 kB | 53/169 kB
Progress (5): 238 kB | 209 kB | 193/502 kB | 229/520 kB | 53/169 kB
Progress (5): 238 kB | 209 kB | 193/502 kB | 229/520 kB | 57/169 kB
Progress (5): 238 kB | 209 kB | 197/502 kB | 229/520 kB | 57/169 kB
Progress (5): 238 kB | 209 kB | 197/502 kB | 233/520 kB | 57/169 kB
                                                                   
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 1.2 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/2.0.5/plexus-utils-2.0.5.jar
Progress (4): 209 kB | 197/502 kB | 233/520 kB | 61/169 kB
Progress (4): 209 kB | 197/502 kB | 238/520 kB | 61/169 kB
Progress (4): 209 kB | 201/502 kB | 238/520 kB | 61/169 kB
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Progress (4): 209 kB | 201/502 kB | 242/520 kB | 66/169 kB
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Progress (4): 209 kB | 205/502 kB | 246/520 kB | 70/169 kB
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Progress (4): 209 kB | 213/502 kB | 258/520 kB | 74/169 kB
Progress (4): 209 kB | 213/502 kB | 258/520 kB | 78/169 kB
Progress (4): 209 kB | 213/502 kB | 262/520 kB | 78/169 kB
Progress (4): 209 kB | 213/502 kB | 262/520 kB | 82/169 kB
Progress (4): 209 kB | 217/502 kB | 262/520 kB | 82/169 kB
Progress (4): 209 kB | 217/502 kB | 266/520 kB | 82/169 kB
Progress (4): 209 kB | 221/502 kB | 266/520 kB | 82/169 kB
Progress (4): 209 kB | 221/502 kB | 270/520 kB | 82/169 kB
Progress (4): 209 kB | 221/502 kB | 270/520 kB | 86/169 kB
                                                          
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Progress (3): 225/502 kB | 270/520 kB | 86/169 kB
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Progress (4): 238/502 kB | 287/520 kB | 102/169 kB | 4.1/223 kB
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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 [  9.212 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [  0.036 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [  0.076 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [  4.527 s]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [  0.204 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [  0.267 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [  0.024 s]
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  16.087 s
[INFO] Finished at: 2020-12-02T19:48:47-08:00
[INFO] ------------------------------------------------------------------------
+ popd
~/workspace/ADAM-prb/HADOOP_VERSION/2.7.5/SCALA_VERSION/2.11/SPARK_VERSION/2.4.7/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/2.11/SPARK_VERSION/2.4.7/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...
[Set GitHub commit status (universal)] SUCCESS on repos [] (sha:e6332ef) with context:ADAM-prb/HADOOP_VERSION=2.7.5,SCALA_VERSION=2.11,SPARK_VERSION=2.4.7,label=ubuntu
Finished: SUCCESS