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@ryan-williams
Created Sep 30, 2015
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ivy race condition in spark
error: could not lock config file /hpc/users/willir31/.gitconfig: File exists
Dynamically requesting 1:1000 executors
Woops: /etc/hadoop/conf.cloudera.yarn/topology.py requires Python 2
Found $PYTHON2_HOME at /hpc/users/willir31/.local; attempting to prepend /hpc/users/willir31/.local/bin to $PATH...
Running command:
/hpc/users/willir31/c/adam/bin/adam-submit --master yarn --deploy-mode client --executor-cores 6 --executor-memory 17g --driver-memory 10g --conf spark.default.parallelism=1000 --conf spark.eventLog.enabled=true --conf spark.eventLog.dir=hdfs://demeter-nn1.demeter.hpc.mssm.edu:/spark/tmp/logs --conf spark.slim.host=hammerlab-dev3.hpc.mssm.edu --conf spark.extraListeners=org.apache.spark.JsonRelay --packages org.hammerlab:spark-json-relay:2.0.0 --conf spark.storage.memoryFraction=0.05 --conf spark.shuffle.memoryFraction=0.4 --conf spark.shuffle.service.enabled=true --conf spark.speculation=true --conf spark.speculation.interval=1000 --conf spark.speculation.multiplier=2 --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.minExecutors=1 --conf spark.dynamicAllocation.initialExecutors=1 --conf spark.dynamicAllocation.maxExecutors=1000 --conf spark.dynamicAllocation.schedulerBacklogTimeout=1 --conf spark.dynamicAllocation.executorIdleTimeout=300 --conf spark.yarn.executor.memoryOverhead=1024 --driver-java-options -Dyarn.resourcemanager.am.max-attempts=1 --conf spark.akka.timeout=120 --conf spark.file.transferTo=false --conf spark.core.connection.ack.wait.timeout=120 --conf spark.ui.enabled=false --executor-cores 10 --executor-memory 5g --driver-memory 1g --conf spark.shuffle.memoryFraction=0.8 -- transform /datasets/illumina_platinum/200x/fastq/ERR174313_1.fastq -paired_fastq /datasets/illumina_platinum/200x/fastq/ERR174313_2.fastq -concat /datasets/illumina_platinum/200x/fastq/ERR174313_unpaired.fastq -record_group ERR174313 /datasets/illumina_platinum/200x/ERR174313.adam
Using SPARK_SUBMIT=/hpc/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/bin/spark-submit
Ivy Default Cache set to: /hpc/users/willir31/.ivy2/cache
The jars for the packages stored in: /hpc/users/willir31/.ivy2/jars
:: loading settings :: url = jar:file:/demeter/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/lib/spark-assembly-1.5.0-hadoop2.6.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
org.hammerlab#spark-json-relay added as a dependency
:: resolving dependencies :: org.apache.spark#spark-submit-parent;1.0
confs: [default]
found org.hammerlab#spark-json-relay;2.0.0 in list
found org.json4s#json4s-jackson_2.10;3.2.10 in list
found org.json4s#json4s-core_2.10;3.2.10 in list
found org.json4s#json4s-ast_2.10;3.2.10 in list
found com.thoughtworks.paranamer#paranamer;2.6 in list
found com.fasterxml.jackson.core#jackson-databind;2.3.1 in list
found com.fasterxml.jackson.core#jackson-annotations;2.3.0 in list
found com.fasterxml.jackson.core#jackson-core;2.3.1 in list
found org.scala-lang#scalap;2.10.4 in list
found org.scala-lang#scala-compiler;2.10.4 in list
found org.scala-lang#scala-reflect;2.10.4 in list
:: resolution report :: resolve 1481ms :: artifacts dl 112ms
:: modules in use:
com.fasterxml.jackson.core#jackson-annotations;2.3.0 from list in [default]
com.fasterxml.jackson.core#jackson-core;2.3.1 from list in [default]
com.fasterxml.jackson.core#jackson-databind;2.3.1 from list in [default]
com.thoughtworks.paranamer#paranamer;2.6 from list in [default]
org.hammerlab#spark-json-relay;2.0.0 from list in [default]
org.json4s#json4s-ast_2.10;3.2.10 from list in [default]
org.json4s#json4s-core_2.10;3.2.10 from list in [default]
org.json4s#json4s-jackson_2.10;3.2.10 from list in [default]
org.scala-lang#scala-compiler;2.10.4 from list in [default]
org.scala-lang#scala-reflect;2.10.4 from list in [default]
org.scala-lang#scalap;2.10.4 from list in [default]
:: evicted modules:
org.scala-lang#scalap;2.10.0 by [org.scala-lang#scalap;2.10.4] in [default]
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 12 | 0 | 0 | 1 || 11 | 0 |
---------------------------------------------------------------------
:: retrieving :: org.apache.spark#spark-submit-parent
confs: [default]
Exception in thread "main" java.lang.RuntimeException: problem during retrieve of org.apache.spark#spark-submit-parent: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Premature end of file.
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:249)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:83)
at org.apache.ivy.Ivy.retrieve(Ivy.java:551)
at org.apache.spark.deploy.SparkSubmitUtils$.resolveMavenCoordinates(SparkSubmit.scala:1006)
at org.apache.spark.deploy.SparkSubmit$.prepareSubmitEnvironment(SparkSubmit.scala:286)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:153)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Premature end of file.
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:293)
at org.apache.ivy.core.retrieve.RetrieveEngine.determineArtifactsToCopy(RetrieveEngine.java:329)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:118)
... 7 more
Caused by: org.xml.sax.SAXParseException; Premature end of file.
at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:328)
at org.apache.ivy.plugins.report.XmlReportParser$SaxXmlReportParser.parse(XmlReportParser.java:249)
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:291)
... 9 more
ln: cannot remove `/hpc/users/willir31/s/yarn/ldl': No such file or directory
ln: cannot remove `/hpc/users/willir31/s/yarn/ycl': No such file or directory
ln: creating symbolic link `/hpc/users/willir31/s/yarn/yll': File exists
error: could not lock config file /hpc/users/willir31/.gitconfig: File exists
Dynamically requesting 1:1000 executors
Woops: /etc/hadoop/conf.cloudera.yarn/topology.py requires Python 2
Found $PYTHON2_HOME at /hpc/users/willir31/.local; attempting to prepend /hpc/users/willir31/.local/bin to $PATH...
Running command:
/hpc/users/willir31/c/adam/bin/adam-submit --master yarn --deploy-mode client --executor-cores 6 --executor-memory 17g --driver-memory 10g --conf spark.default.parallelism=1000 --conf spark.eventLog.enabled=true --conf spark.eventLog.dir=hdfs://demeter-nn1.demeter.hpc.mssm.edu:/spark/tmp/logs --conf spark.slim.host=hammerlab-dev3.hpc.mssm.edu --conf spark.extraListeners=org.apache.spark.JsonRelay --packages org.hammerlab:spark-json-relay:2.0.0 --conf spark.storage.memoryFraction=0.05 --conf spark.shuffle.memoryFraction=0.4 --conf spark.shuffle.service.enabled=true --conf spark.speculation=true --conf spark.speculation.interval=1000 --conf spark.speculation.multiplier=2 --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.minExecutors=1 --conf spark.dynamicAllocation.initialExecutors=1 --conf spark.dynamicAllocation.maxExecutors=1000 --conf spark.dynamicAllocation.schedulerBacklogTimeout=1 --conf spark.dynamicAllocation.executorIdleTimeout=300 --conf spark.yarn.executor.memoryOverhead=1024 --driver-java-options -Dyarn.resourcemanager.am.max-attempts=1 --conf spark.akka.timeout=120 --conf spark.file.transferTo=false --conf spark.core.connection.ack.wait.timeout=120 --conf spark.ui.enabled=false --executor-cores 10 --executor-memory 5g --driver-memory 1g --conf spark.shuffle.memoryFraction=0.8 -- transform /datasets/illumina_platinum/200x/fastq/ERR174314_1.fastq -paired_fastq /datasets/illumina_platinum/200x/fastq/ERR174314_2.fastq -concat /datasets/illumina_platinum/200x/fastq/ERR174314_unpaired.fastq -record_group ERR174314 /datasets/illumina_platinum/200x/ERR174314.adam
Using SPARK_SUBMIT=/hpc/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/bin/spark-submit
Ivy Default Cache set to: /hpc/users/willir31/.ivy2/cache
The jars for the packages stored in: /hpc/users/willir31/.ivy2/jars
:: loading settings :: url = jar:file:/demeter/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/lib/spark-assembly-1.5.0-hadoop2.6.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
org.hammerlab#spark-json-relay added as a dependency
:: resolving dependencies :: org.apache.spark#spark-submit-parent;1.0
confs: [default]
found org.hammerlab#spark-json-relay;2.0.0 in list
found org.json4s#json4s-jackson_2.10;3.2.10 in list
found org.json4s#json4s-core_2.10;3.2.10 in list
found org.json4s#json4s-ast_2.10;3.2.10 in list
found com.thoughtworks.paranamer#paranamer;2.6 in list
found com.fasterxml.jackson.core#jackson-databind;2.3.1 in list
found com.fasterxml.jackson.core#jackson-annotations;2.3.0 in list
found com.fasterxml.jackson.core#jackson-core;2.3.1 in list
found org.scala-lang#scalap;2.10.4 in list
found org.scala-lang#scala-compiler;2.10.4 in list
found org.scala-lang#scala-reflect;2.10.4 in list
:: resolution report :: resolve 1525ms :: artifacts dl 65ms
:: modules in use:
com.fasterxml.jackson.core#jackson-annotations;2.3.0 from list in [default]
com.fasterxml.jackson.core#jackson-core;2.3.1 from list in [default]
com.fasterxml.jackson.core#jackson-databind;2.3.1 from list in [default]
com.thoughtworks.paranamer#paranamer;2.6 from list in [default]
org.hammerlab#spark-json-relay;2.0.0 from list in [default]
org.json4s#json4s-ast_2.10;3.2.10 from list in [default]
org.json4s#json4s-core_2.10;3.2.10 from list in [default]
org.json4s#json4s-jackson_2.10;3.2.10 from list in [default]
org.scala-lang#scala-compiler;2.10.4 from list in [default]
org.scala-lang#scala-reflect;2.10.4 from list in [default]
org.scala-lang#scalap;2.10.4 from list in [default]
:: evicted modules:
org.scala-lang#scalap;2.10.0 by [org.scala-lang#scalap;2.10.4] in [default]
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 12 | 0 | 0 | 1 || 11 | 0 |
---------------------------------------------------------------------
:: retrieving :: org.apache.spark#spark-submit-parent
confs: [default]
Exception in thread "main" java.lang.RuntimeException: problem during retrieve of org.apache.spark#spark-submit-parent: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Premature end of file.
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:249)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:83)
at org.apache.ivy.Ivy.retrieve(Ivy.java:551)
at org.apache.spark.deploy.SparkSubmitUtils$.resolveMavenCoordinates(SparkSubmit.scala:1006)
at org.apache.spark.deploy.SparkSubmit$.prepareSubmitEnvironment(SparkSubmit.scala:286)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:153)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Premature end of file.
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:293)
at org.apache.ivy.core.retrieve.RetrieveEngine.determineArtifactsToCopy(RetrieveEngine.java:329)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:118)
... 7 more
Caused by: org.xml.sax.SAXParseException; Premature end of file.
at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:328)
at org.apache.ivy.plugins.report.XmlReportParser$SaxXmlReportParser.parse(XmlReportParser.java:249)
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:291)
... 9 more
error: could not lock config file /hpc/users/willir31/.gitconfig: File exists
Dynamically requesting 1:1000 executors
Woops: /etc/hadoop/conf.cloudera.yarn/topology.py requires Python 2
Found $PYTHON2_HOME at /hpc/users/willir31/.local; attempting to prepend /hpc/users/willir31/.local/bin to $PATH...
Running command:
/hpc/users/willir31/c/adam/bin/adam-submit --master yarn --deploy-mode client --executor-cores 6 --executor-memory 17g --driver-memory 10g --conf spark.default.parallelism=1000 --conf spark.eventLog.enabled=true --conf spark.eventLog.dir=hdfs://demeter-nn1.demeter.hpc.mssm.edu:/spark/tmp/logs --conf spark.slim.host=hammerlab-dev3.hpc.mssm.edu --conf spark.extraListeners=org.apache.spark.JsonRelay --packages org.hammerlab:spark-json-relay:2.0.0 --conf spark.storage.memoryFraction=0.05 --conf spark.shuffle.memoryFraction=0.4 --conf spark.shuffle.service.enabled=true --conf spark.speculation=true --conf spark.speculation.interval=1000 --conf spark.speculation.multiplier=2 --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.minExecutors=1 --conf spark.dynamicAllocation.initialExecutors=1 --conf spark.dynamicAllocation.maxExecutors=1000 --conf spark.dynamicAllocation.schedulerBacklogTimeout=1 --conf spark.dynamicAllocation.executorIdleTimeout=300 --conf spark.yarn.executor.memoryOverhead=1024 --driver-java-options -Dyarn.resourcemanager.am.max-attempts=1 --conf spark.akka.timeout=120 --conf spark.file.transferTo=false --conf spark.core.connection.ack.wait.timeout=120 --conf spark.ui.enabled=false --executor-cores 10 --executor-memory 5g --driver-memory 1g --conf spark.shuffle.memoryFraction=0.8 -- transform /datasets/illumina_platinum/200x/fastq/ERR174332_1.fastq -paired_fastq /datasets/illumina_platinum/200x/fastq/ERR174332_2.fastq -concat /datasets/illumina_platinum/200x/fastq/ERR174332_unpaired.fastq -record_group ERR174332 -stringency SILENT /datasets/illumina_platinum/200x/ERR174332.adam
Using SPARK_SUBMIT=/hpc/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/bin/spark-submit
Ivy Default Cache set to: /hpc/users/willir31/.ivy2/cache
The jars for the packages stored in: /hpc/users/willir31/.ivy2/jars
:: loading settings :: url = jar:file:/demeter/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/lib/spark-assembly-1.5.0-hadoop2.6.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
org.hammerlab#spark-json-relay added as a dependency
:: resolving dependencies :: org.apache.spark#spark-submit-parent;1.0
confs: [default]
found org.hammerlab#spark-json-relay;2.0.0 in list
found org.json4s#json4s-jackson_2.10;3.2.10 in list
found org.json4s#json4s-core_2.10;3.2.10 in list
found org.json4s#json4s-ast_2.10;3.2.10 in list
found com.thoughtworks.paranamer#paranamer;2.6 in list
found com.fasterxml.jackson.core#jackson-databind;2.3.1 in list
found com.fasterxml.jackson.core#jackson-annotations;2.3.0 in list
found com.fasterxml.jackson.core#jackson-core;2.3.1 in list
found org.scala-lang#scalap;2.10.4 in list
found org.scala-lang#scala-compiler;2.10.4 in list
found org.scala-lang#scala-reflect;2.10.4 in list
:: resolution report :: resolve 1581ms :: artifacts dl 65ms
:: modules in use:
com.fasterxml.jackson.core#jackson-annotations;2.3.0 from list in [default]
com.fasterxml.jackson.core#jackson-core;2.3.1 from list in [default]
com.fasterxml.jackson.core#jackson-databind;2.3.1 from list in [default]
com.thoughtworks.paranamer#paranamer;2.6 from list in [default]
org.hammerlab#spark-json-relay;2.0.0 from list in [default]
org.json4s#json4s-ast_2.10;3.2.10 from list in [default]
org.json4s#json4s-core_2.10;3.2.10 from list in [default]
org.json4s#json4s-jackson_2.10;3.2.10 from list in [default]
org.scala-lang#scala-compiler;2.10.4 from list in [default]
org.scala-lang#scala-reflect;2.10.4 from list in [default]
org.scala-lang#scalap;2.10.4 from list in [default]
:: evicted modules:
org.scala-lang#scalap;2.10.0 by [org.scala-lang#scalap;2.10.4] in [default]
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 12 | 0 | 0 | 1 || 11 | 0 |
---------------------------------------------------------------------
:: retrieving :: org.apache.spark#spark-submit-parent
confs: [default]
Exception in thread "main" java.lang.RuntimeException: problem during retrieve of org.apache.spark#spark-submit-parent: java.lang.IllegalStateException: Report file '/hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml' does not exist.
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:249)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:83)
at org.apache.ivy.Ivy.retrieve(Ivy.java:551)
at org.apache.spark.deploy.SparkSubmitUtils$.resolveMavenCoordinates(SparkSubmit.scala:1006)
at org.apache.spark.deploy.SparkSubmit$.prepareSubmitEnvironment(SparkSubmit.scala:286)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:153)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.lang.IllegalStateException: Report file '/hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml' does not exist.
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:285)
at org.apache.ivy.core.retrieve.RetrieveEngine.determineArtifactsToCopy(RetrieveEngine.java:329)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:118)
... 7 more
Dynamically requesting 1:1000 executors
Woops: /etc/hadoop/conf.cloudera.yarn/topology.py requires Python 2
Found $PYTHON2_HOME at /hpc/users/willir31/.local; attempting to prepend /hpc/users/willir31/.local/bin to $PATH...
Running command:
/hpc/users/willir31/c/adam/bin/adam-submit --master yarn --deploy-mode client --executor-cores 6 --executor-memory 17g --driver-memory 10g --conf spark.default.parallelism=1000 --conf spark.eventLog.enabled=true --conf spark.eventLog.dir=hdfs://demeter-nn1.demeter.hpc.mssm.edu:/spark/tmp/logs --conf spark.slim.host=hammerlab-dev3.hpc.mssm.edu --conf spark.extraListeners=org.apache.spark.JsonRelay --packages org.hammerlab:spark-json-relay:2.0.0 --conf spark.storage.memoryFraction=0.05 --conf spark.shuffle.memoryFraction=0.4 --conf spark.shuffle.service.enabled=true --conf spark.speculation=true --conf spark.speculation.interval=1000 --conf spark.speculation.multiplier=2 --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.minExecutors=1 --conf spark.dynamicAllocation.initialExecutors=1 --conf spark.dynamicAllocation.maxExecutors=1000 --conf spark.dynamicAllocation.schedulerBacklogTimeout=1 --conf spark.dynamicAllocation.executorIdleTimeout=300 --conf spark.yarn.executor.memoryOverhead=1024 --driver-java-options -Dyarn.resourcemanager.am.max-attempts=1 --conf spark.akka.timeout=120 --conf spark.file.transferTo=false --conf spark.core.connection.ack.wait.timeout=120 --conf spark.ui.enabled=false --executor-cores 10 --executor-memory 5g --driver-memory 1g --conf spark.shuffle.memoryFraction=0.8 -- transform /datasets/illumina_platinum/200x/fastq/ERR174335_1.fastq -paired_fastq /datasets/illumina_platinum/200x/fastq/ERR174335_2.fastq -concat /datasets/illumina_platinum/200x/fastq/ERR174335_unpaired.fastq -record_group ERR174335 -stringency SILENT /datasets/illumina_platinum/200x/ERR174335.adam
Using SPARK_SUBMIT=/hpc/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/bin/spark-submit
Ivy Default Cache set to: /hpc/users/willir31/.ivy2/cache
The jars for the packages stored in: /hpc/users/willir31/.ivy2/jars
:: loading settings :: url = jar:file:/demeter/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/lib/spark-assembly-1.5.0-hadoop2.6.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
org.hammerlab#spark-json-relay added as a dependency
:: resolving dependencies :: org.apache.spark#spark-submit-parent;1.0
confs: [default]
found org.hammerlab#spark-json-relay;2.0.0 in list
found org.json4s#json4s-jackson_2.10;3.2.10 in list
found org.json4s#json4s-core_2.10;3.2.10 in list
found org.json4s#json4s-ast_2.10;3.2.10 in list
found com.thoughtworks.paranamer#paranamer;2.6 in list
found com.fasterxml.jackson.core#jackson-databind;2.3.1 in list
found com.fasterxml.jackson.core#jackson-annotations;2.3.0 in list
found com.fasterxml.jackson.core#jackson-core;2.3.1 in list
found org.scala-lang#scalap;2.10.4 in list
found org.scala-lang#scala-compiler;2.10.4 in list
found org.scala-lang#scala-reflect;2.10.4 in list
:: resolution report :: resolve 1678ms :: artifacts dl 87ms
:: modules in use:
com.fasterxml.jackson.core#jackson-annotations;2.3.0 from list in [default]
com.fasterxml.jackson.core#jackson-core;2.3.1 from list in [default]
com.fasterxml.jackson.core#jackson-databind;2.3.1 from list in [default]
com.thoughtworks.paranamer#paranamer;2.6 from list in [default]
org.hammerlab#spark-json-relay;2.0.0 from list in [default]
org.json4s#json4s-ast_2.10;3.2.10 from list in [default]
org.json4s#json4s-core_2.10;3.2.10 from list in [default]
org.json4s#json4s-jackson_2.10;3.2.10 from list in [default]
org.scala-lang#scala-compiler;2.10.4 from list in [default]
org.scala-lang#scala-reflect;2.10.4 from list in [default]
org.scala-lang#scalap;2.10.4 from list in [default]
:: evicted modules:
org.scala-lang#scalap;2.10.0 by [org.scala-lang#scalap;2.10.4] in [default]
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 12 | 0 | 0 | 1 || 11 | 0 |
---------------------------------------------------------------------
:: retrieving :: org.apache.spark#spark-submit-parent
confs: [default]
Exception in thread "main" java.lang.RuntimeException: problem during retrieve of org.apache.spark#spark-submit-parent: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Premature end of file.
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:249)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:83)
at org.apache.ivy.Ivy.retrieve(Ivy.java:551)
at org.apache.spark.deploy.SparkSubmitUtils$.resolveMavenCoordinates(SparkSubmit.scala:1006)
at org.apache.spark.deploy.SparkSubmit$.prepareSubmitEnvironment(SparkSubmit.scala:286)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:153)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Premature end of file.
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:293)
at org.apache.ivy.core.retrieve.RetrieveEngine.determineArtifactsToCopy(RetrieveEngine.java:329)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:118)
... 7 more
Caused by: org.xml.sax.SAXParseException; Premature end of file.
at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:328)
at org.apache.ivy.plugins.report.XmlReportParser$SaxXmlReportParser.parse(XmlReportParser.java:249)
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:291)
... 9 more
error: could not lock config file /hpc/users/willir31/.gitconfig: File exists
Dynamically requesting 1:1000 executors
Woops: /etc/hadoop/conf.cloudera.yarn/topology.py requires Python 2
Found $PYTHON2_HOME at /hpc/users/willir31/.local; attempting to prepend /hpc/users/willir31/.local/bin to $PATH...
Running command:
/hpc/users/willir31/c/adam/bin/adam-submit --master yarn --deploy-mode client --executor-cores 6 --executor-memory 17g --driver-memory 10g --conf spark.default.parallelism=1000 --conf spark.eventLog.enabled=true --conf spark.eventLog.dir=hdfs://demeter-nn1.demeter.hpc.mssm.edu:/spark/tmp/logs --conf spark.slim.host=hammerlab-dev3.hpc.mssm.edu --conf spark.extraListeners=org.apache.spark.JsonRelay --packages org.hammerlab:spark-json-relay:2.0.0 --conf spark.storage.memoryFraction=0.05 --conf spark.shuffle.memoryFraction=0.4 --conf spark.shuffle.service.enabled=true --conf spark.speculation=true --conf spark.speculation.interval=1000 --conf spark.speculation.multiplier=2 --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.minExecutors=1 --conf spark.dynamicAllocation.initialExecutors=1 --conf spark.dynamicAllocation.maxExecutors=1000 --conf spark.dynamicAllocation.schedulerBacklogTimeout=1 --conf spark.dynamicAllocation.executorIdleTimeout=300 --conf spark.yarn.executor.memoryOverhead=1024 --driver-java-options -Dyarn.resourcemanager.am.max-attempts=1 --conf spark.akka.timeout=120 --conf spark.file.transferTo=false --conf spark.core.connection.ack.wait.timeout=120 --conf spark.ui.enabled=false --executor-cores 10 --executor-memory 5g --driver-memory 1g --conf spark.shuffle.memoryFraction=0.8 -- transform /datasets/illumina_platinum/200x/fastq/ERR174336_1.fastq -paired_fastq /datasets/illumina_platinum/200x/fastq/ERR174336_2.fastq -concat /datasets/illumina_platinum/200x/fastq/ERR174336_unpaired.fastq -record_group ERR174336 -stringency SILENT /datasets/illumina_platinum/200x/ERR174336.adam
Using SPARK_SUBMIT=/hpc/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/bin/spark-submit
Ivy Default Cache set to: /hpc/users/willir31/.ivy2/cache
The jars for the packages stored in: /hpc/users/willir31/.ivy2/jars
:: loading settings :: url = jar:file:/demeter/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/lib/spark-assembly-1.5.0-hadoop2.6.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
org.hammerlab#spark-json-relay added as a dependency
:: resolving dependencies :: org.apache.spark#spark-submit-parent;1.0
confs: [default]
found org.hammerlab#spark-json-relay;2.0.0 in list
found org.json4s#json4s-jackson_2.10;3.2.10 in list
found org.json4s#json4s-core_2.10;3.2.10 in list
found org.json4s#json4s-ast_2.10;3.2.10 in list
found com.thoughtworks.paranamer#paranamer;2.6 in list
found com.fasterxml.jackson.core#jackson-databind;2.3.1 in list
found com.fasterxml.jackson.core#jackson-annotations;2.3.0 in list
found com.fasterxml.jackson.core#jackson-core;2.3.1 in list
found org.scala-lang#scalap;2.10.4 in list
found org.scala-lang#scala-compiler;2.10.4 in list
found org.scala-lang#scala-reflect;2.10.4 in list
:: resolution report :: resolve 2273ms :: artifacts dl 46ms
:: modules in use:
com.fasterxml.jackson.core#jackson-annotations;2.3.0 from list in [default]
com.fasterxml.jackson.core#jackson-core;2.3.1 from list in [default]
com.fasterxml.jackson.core#jackson-databind;2.3.1 from list in [default]
com.thoughtworks.paranamer#paranamer;2.6 from list in [default]
org.hammerlab#spark-json-relay;2.0.0 from list in [default]
org.json4s#json4s-ast_2.10;3.2.10 from list in [default]
org.json4s#json4s-core_2.10;3.2.10 from list in [default]
org.json4s#json4s-jackson_2.10;3.2.10 from list in [default]
org.scala-lang#scala-compiler;2.10.4 from list in [default]
org.scala-lang#scala-reflect;2.10.4 from list in [default]
org.scala-lang#scalap;2.10.4 from list in [default]
:: evicted modules:
org.scala-lang#scalap;2.10.0 by [org.scala-lang#scalap;2.10.4] in [default]
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 12 | 0 | 0 | 1 || 11 | 0 |
---------------------------------------------------------------------
:: retrieving :: org.apache.spark#spark-submit-parent
confs: [default]
Exception in thread "main" java.lang.RuntimeException: problem during retrieve of org.apache.spark#spark-submit-parent: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Premature end of file.
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:249)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:83)
at org.apache.ivy.Ivy.retrieve(Ivy.java:551)
at org.apache.spark.deploy.SparkSubmitUtils$.resolveMavenCoordinates(SparkSubmit.scala:1006)
at org.apache.spark.deploy.SparkSubmit$.prepareSubmitEnvironment(SparkSubmit.scala:286)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:153)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Premature end of file.
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:293)
at org.apache.ivy.core.retrieve.RetrieveEngine.determineArtifactsToCopy(RetrieveEngine.java:329)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:118)
... 7 more
Caused by: org.xml.sax.SAXParseException; Premature end of file.
at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:328)
at org.apache.ivy.plugins.report.XmlReportParser$SaxXmlReportParser.parse(XmlReportParser.java:249)
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:291)
... 9 more
ln: cannot remove `/hpc/users/willir31/s/yarn/ldl': No such file or directory
ln: cannot remove `/hpc/users/willir31/s/yarn/ya': No such file or directory
Dynamically requesting 1:1000 executors
Woops: /etc/hadoop/conf.cloudera.yarn/topology.py requires Python 2
Found $PYTHON2_HOME at /hpc/users/willir31/.local; attempting to prepend /hpc/users/willir31/.local/bin to $PATH...
Running command:
/hpc/users/willir31/c/adam/bin/adam-submit --master yarn --deploy-mode client --executor-cores 6 --executor-memory 17g --driver-memory 10g --conf spark.default.parallelism=1000 --conf spark.eventLog.enabled=true --conf spark.eventLog.dir=hdfs://demeter-nn1.demeter.hpc.mssm.edu:/spark/tmp/logs --conf spark.slim.host=hammerlab-dev3.hpc.mssm.edu --conf spark.extraListeners=org.apache.spark.JsonRelay --packages org.hammerlab:spark-json-relay:2.0.0 --conf spark.storage.memoryFraction=0.05 --conf spark.shuffle.memoryFraction=0.4 --conf spark.shuffle.service.enabled=true --conf spark.speculation=true --conf spark.speculation.interval=1000 --conf spark.speculation.multiplier=2 --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.minExecutors=1 --conf spark.dynamicAllocation.initialExecutors=1 --conf spark.dynamicAllocation.maxExecutors=1000 --conf spark.dynamicAllocation.schedulerBacklogTimeout=1 --conf spark.dynamicAllocation.executorIdleTimeout=300 --conf spark.yarn.executor.memoryOverhead=1024 --driver-java-options -Dyarn.resourcemanager.am.max-attempts=1 --conf spark.akka.timeout=120 --conf spark.file.transferTo=false --conf spark.core.connection.ack.wait.timeout=120 --conf spark.ui.enabled=false --executor-cores 10 --executor-memory 5g --driver-memory 1g --conf spark.shuffle.memoryFraction=0.8 -- transform /datasets/illumina_platinum/200x/fastq/ERR174340_1.fastq -paired_fastq /datasets/illumina_platinum/200x/fastq/ERR174340_2.fastq -concat /datasets/illumina_platinum/200x/fastq/ERR174340_unpaired.fastq -record_group ERR174340 -stringency SILENT /datasets/illumina_platinum/200x/ERR174340.adam
Using SPARK_SUBMIT=/hpc/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/bin/spark-submit
Ivy Default Cache set to: /hpc/users/willir31/.ivy2/cache
The jars for the packages stored in: /hpc/users/willir31/.ivy2/jars
:: loading settings :: url = jar:file:/demeter/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/lib/spark-assembly-1.5.0-hadoop2.6.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
org.hammerlab#spark-json-relay added as a dependency
:: resolving dependencies :: org.apache.spark#spark-submit-parent;1.0
confs: [default]
found org.hammerlab#spark-json-relay;2.0.0 in list
found org.json4s#json4s-jackson_2.10;3.2.10 in list
found org.json4s#json4s-core_2.10;3.2.10 in list
found org.json4s#json4s-ast_2.10;3.2.10 in list
found com.thoughtworks.paranamer#paranamer;2.6 in list
found com.fasterxml.jackson.core#jackson-databind;2.3.1 in list
found com.fasterxml.jackson.core#jackson-annotations;2.3.0 in list
found com.fasterxml.jackson.core#jackson-core;2.3.1 in list
found org.scala-lang#scalap;2.10.4 in list
found org.scala-lang#scala-compiler;2.10.4 in list
found org.scala-lang#scala-reflect;2.10.4 in list
:: resolution report :: resolve 1870ms :: artifacts dl 113ms
:: modules in use:
com.fasterxml.jackson.core#jackson-annotations;2.3.0 from list in [default]
com.fasterxml.jackson.core#jackson-core;2.3.1 from list in [default]
com.fasterxml.jackson.core#jackson-databind;2.3.1 from list in [default]
com.thoughtworks.paranamer#paranamer;2.6 from list in [default]
org.hammerlab#spark-json-relay;2.0.0 from list in [default]
org.json4s#json4s-ast_2.10;3.2.10 from list in [default]
org.json4s#json4s-core_2.10;3.2.10 from list in [default]
org.json4s#json4s-jackson_2.10;3.2.10 from list in [default]
org.scala-lang#scala-compiler;2.10.4 from list in [default]
org.scala-lang#scala-reflect;2.10.4 from list in [default]
org.scala-lang#scalap;2.10.4 from list in [default]
:: evicted modules:
org.scala-lang#scalap;2.10.0 by [org.scala-lang#scalap;2.10.4] in [default]
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 12 | 0 | 0 | 1 || 11 | 0 |
---------------------------------------------------------------------
:: retrieving :: org.apache.spark#spark-submit-parent
confs: [default]
Exception in thread "main" java.lang.RuntimeException: problem during retrieve of org.apache.spark#spark-submit-parent: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml (No such file or directory)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:249)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:83)
at org.apache.ivy.Ivy.retrieve(Ivy.java:551)
at org.apache.spark.deploy.SparkSubmitUtils$.resolveMavenCoordinates(SparkSubmit.scala:1006)
at org.apache.spark.deploy.SparkSubmit$.prepareSubmitEnvironment(SparkSubmit.scala:286)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:153)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml (No such file or directory)
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:293)
at org.apache.ivy.core.retrieve.RetrieveEngine.determineArtifactsToCopy(RetrieveEngine.java:329)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:118)
... 7 more
Caused by: java.io.FileNotFoundException: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml (No such file or directory)
at java.io.FileInputStream.open(Native Method)
at java.io.FileInputStream.<init>(FileInputStream.java:146)
at java.io.FileInputStream.<init>(FileInputStream.java:101)
at sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:90)
at sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:188)
at org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Unknown Source)
at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:328)
at org.apache.ivy.plugins.report.XmlReportParser$SaxXmlReportParser.parse(XmlReportParser.java:249)
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:291)
... 9 more
error: could not lock config file /hpc/users/willir31/.gitconfig: File exists
Dynamically requesting 1:1000 executors
Woops: /etc/hadoop/conf.cloudera.yarn/topology.py requires Python 2
Found $PYTHON2_HOME at /hpc/users/willir31/.local; attempting to prepend /hpc/users/willir31/.local/bin to $PATH...
Running command:
/hpc/users/willir31/c/adam/bin/adam-submit --master yarn --deploy-mode client --executor-cores 6 --executor-memory 17g --driver-memory 10g --conf spark.default.parallelism=1000 --conf spark.eventLog.enabled=true --conf spark.eventLog.dir=hdfs://demeter-nn1.demeter.hpc.mssm.edu:/spark/tmp/logs --conf spark.slim.host=hammerlab-dev3.hpc.mssm.edu --conf spark.extraListeners=org.apache.spark.JsonRelay --packages org.hammerlab:spark-json-relay:2.0.0 --conf spark.storage.memoryFraction=0.05 --conf spark.shuffle.memoryFraction=0.4 --conf spark.shuffle.service.enabled=true --conf spark.speculation=true --conf spark.speculation.interval=1000 --conf spark.speculation.multiplier=2 --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.minExecutors=1 --conf spark.dynamicAllocation.initialExecutors=1 --conf spark.dynamicAllocation.maxExecutors=1000 --conf spark.dynamicAllocation.schedulerBacklogTimeout=1 --conf spark.dynamicAllocation.executorIdleTimeout=300 --conf spark.yarn.executor.memoryOverhead=1024 --driver-java-options -Dyarn.resourcemanager.am.max-attempts=1 --conf spark.akka.timeout=120 --conf spark.file.transferTo=false --conf spark.core.connection.ack.wait.timeout=120 --conf spark.ui.enabled=false --executor-cores 10 --executor-memory 5g --driver-memory 1g --conf spark.shuffle.memoryFraction=0.8 -- transform /datasets/illumina_platinum/200x/fastq/ERR174346_1.fastq -paired_fastq /datasets/illumina_platinum/200x/fastq/ERR174346_2.fastq -concat /datasets/illumina_platinum/200x/fastq/ERR174346_unpaired.fastq -record_group ERR174346 -stringency SILENT /datasets/illumina_platinum/200x/ERR174346.adam
Using SPARK_SUBMIT=/hpc/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/bin/spark-submit
Ivy Default Cache set to: /hpc/users/willir31/.ivy2/cache
The jars for the packages stored in: /hpc/users/willir31/.ivy2/jars
:: loading settings :: url = jar:file:/demeter/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/lib/spark-assembly-1.5.0-hadoop2.6.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
org.hammerlab#spark-json-relay added as a dependency
:: resolving dependencies :: org.apache.spark#spark-submit-parent;1.0
confs: [default]
found org.hammerlab#spark-json-relay;2.0.0 in list
found org.json4s#json4s-jackson_2.10;3.2.10 in list
found org.json4s#json4s-core_2.10;3.2.10 in list
found org.json4s#json4s-ast_2.10;3.2.10 in list
found com.thoughtworks.paranamer#paranamer;2.6 in list
found com.fasterxml.jackson.core#jackson-databind;2.3.1 in list
found com.fasterxml.jackson.core#jackson-annotations;2.3.0 in list
found com.fasterxml.jackson.core#jackson-core;2.3.1 in list
found org.scala-lang#scalap;2.10.4 in list
found org.scala-lang#scala-compiler;2.10.4 in list
found org.scala-lang#scala-reflect;2.10.4 in list
:: resolution report :: resolve 1298ms :: artifacts dl 104ms
:: modules in use:
com.fasterxml.jackson.core#jackson-annotations;2.3.0 from list in [default]
com.fasterxml.jackson.core#jackson-core;2.3.1 from list in [default]
com.fasterxml.jackson.core#jackson-databind;2.3.1 from list in [default]
com.thoughtworks.paranamer#paranamer;2.6 from list in [default]
org.hammerlab#spark-json-relay;2.0.0 from list in [default]
org.json4s#json4s-ast_2.10;3.2.10 from list in [default]
org.json4s#json4s-core_2.10;3.2.10 from list in [default]
org.json4s#json4s-jackson_2.10;3.2.10 from list in [default]
org.scala-lang#scala-compiler;2.10.4 from list in [default]
org.scala-lang#scala-reflect;2.10.4 from list in [default]
org.scala-lang#scalap;2.10.4 from list in [default]
:: evicted modules:
org.scala-lang#scalap;2.10.0 by [org.scala-lang#scalap;2.10.4] in [default]
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 12 | 0 | 0 | 1 || 11 | 0 |
---------------------------------------------------------------------
:: problems summary ::
:::: ERRORS
unknown resolver null
unknown resolver null
:: USE VERBOSE OR DEBUG MESSAGE LEVEL FOR MORE DETAILS
:: retrieving :: org.apache.spark#spark-submit-parent
confs: [default]
Exception in thread "main" java.lang.RuntimeException: problem during retrieve of org.apache.spark#spark-submit-parent: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Premature end of file.
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:249)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:83)
at org.apache.ivy.Ivy.retrieve(Ivy.java:551)
at org.apache.spark.deploy.SparkSubmitUtils$.resolveMavenCoordinates(SparkSubmit.scala:1006)
at org.apache.spark.deploy.SparkSubmit$.prepareSubmitEnvironment(SparkSubmit.scala:286)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:153)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Premature end of file.
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:293)
at org.apache.ivy.core.retrieve.RetrieveEngine.determineArtifactsToCopy(RetrieveEngine.java:329)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:118)
... 7 more
Caused by: org.xml.sax.SAXParseException; Premature end of file.
at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:328)
at org.apache.ivy.plugins.report.XmlReportParser$SaxXmlReportParser.parse(XmlReportParser.java:249)
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:291)
... 9 more
ln: creating symbolic link `/hpc/users/willir31/s/yarn/ldl': File exists
ln: cannot remove `/hpc/users/willir31/s/yarn/yl': No such file or directory
Dynamically requesting 1:1000 executors
Woops: /etc/hadoop/conf.cloudera.yarn/topology.py requires Python 2
Found $PYTHON2_HOME at /hpc/users/willir31/.local; attempting to prepend /hpc/users/willir31/.local/bin to $PATH...
Running command:
/hpc/users/willir31/c/adam/bin/adam-submit --master yarn --deploy-mode client --executor-cores 6 --executor-memory 17g --driver-memory 10g --conf spark.default.parallelism=1000 --conf spark.eventLog.enabled=true --conf spark.eventLog.dir=hdfs://demeter-nn1.demeter.hpc.mssm.edu:/spark/tmp/logs --conf spark.slim.host=hammerlab-dev3.hpc.mssm.edu --conf spark.extraListeners=org.apache.spark.JsonRelay --packages org.hammerlab:spark-json-relay:2.0.0 --conf spark.storage.memoryFraction=0.05 --conf spark.shuffle.memoryFraction=0.4 --conf spark.shuffle.service.enabled=true --conf spark.speculation=true --conf spark.speculation.interval=1000 --conf spark.speculation.multiplier=2 --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.minExecutors=1 --conf spark.dynamicAllocation.initialExecutors=1 --conf spark.dynamicAllocation.maxExecutors=1000 --conf spark.dynamicAllocation.schedulerBacklogTimeout=1 --conf spark.dynamicAllocation.executorIdleTimeout=300 --conf spark.yarn.executor.memoryOverhead=1024 --driver-java-options -Dyarn.resourcemanager.am.max-attempts=1 --conf spark.akka.timeout=120 --conf spark.file.transferTo=false --conf spark.core.connection.ack.wait.timeout=120 --conf spark.ui.enabled=false --executor-cores 10 --executor-memory 5g --driver-memory 1g --conf spark.shuffle.memoryFraction=0.8 -- transform /datasets/illumina_platinum/200x/fastq/ERR174364_1.fastq -paired_fastq /datasets/illumina_platinum/200x/fastq/ERR174364_2.fastq -concat /datasets/illumina_platinum/200x/fastq/ERR174364_unpaired.fastq -record_group ERR174364 -stringency SILENT /datasets/illumina_platinum/200x/ERR174364.adam
Using SPARK_SUBMIT=/hpc/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/bin/spark-submit
Ivy Default Cache set to: /hpc/users/willir31/.ivy2/cache
The jars for the packages stored in: /hpc/users/willir31/.ivy2/jars
:: loading settings :: url = jar:file:/demeter/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/lib/spark-assembly-1.5.0-hadoop2.6.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
org.hammerlab#spark-json-relay added as a dependency
:: resolving dependencies :: org.apache.spark#spark-submit-parent;1.0
confs: [default]
found org.hammerlab#spark-json-relay;2.0.0 in list
found org.json4s#json4s-jackson_2.10;3.2.10 in list
found org.json4s#json4s-core_2.10;3.2.10 in list
found org.json4s#json4s-ast_2.10;3.2.10 in list
found com.thoughtworks.paranamer#paranamer;2.6 in list
found com.fasterxml.jackson.core#jackson-databind;2.3.1 in list
found com.fasterxml.jackson.core#jackson-annotations;2.3.0 in list
found com.fasterxml.jackson.core#jackson-core;2.3.1 in list
found org.scala-lang#scalap;2.10.4 in list
found org.scala-lang#scala-compiler;2.10.4 in list
found org.scala-lang#scala-reflect;2.10.4 in list
:: resolution report :: resolve 2466ms :: artifacts dl 129ms
:: modules in use:
com.fasterxml.jackson.core#jackson-annotations;2.3.0 from list in [default]
com.fasterxml.jackson.core#jackson-core;2.3.1 from list in [default]
com.fasterxml.jackson.core#jackson-databind;2.3.1 from list in [default]
com.thoughtworks.paranamer#paranamer;2.6 from list in [default]
org.hammerlab#spark-json-relay;2.0.0 from list in [default]
org.json4s#json4s-ast_2.10;3.2.10 from list in [default]
org.json4s#json4s-core_2.10;3.2.10 from list in [default]
org.json4s#json4s-jackson_2.10;3.2.10 from list in [default]
org.scala-lang#scala-compiler;2.10.4 from list in [default]
org.scala-lang#scala-reflect;2.10.4 from list in [default]
org.scala-lang#scalap;2.10.4 from list in [default]
:: evicted modules:
org.scala-lang#scalap;2.10.0 by [org.scala-lang#scalap;2.10.4] in [default]
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 12 | 0 | 0 | 1 || 11 | 0 |
---------------------------------------------------------------------
:: retrieving :: org.apache.spark#spark-submit-parent
confs: [default]
Exception in thread "main" java.lang.RuntimeException: problem during retrieve of org.apache.spark#spark-submit-parent: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Content is not allowed in prolog.
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:249)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:83)
at org.apache.ivy.Ivy.retrieve(Ivy.java:551)
at org.apache.spark.deploy.SparkSubmitUtils$.resolveMavenCoordinates(SparkSubmit.scala:1006)
at org.apache.spark.deploy.SparkSubmit$.prepareSubmitEnvironment(SparkSubmit.scala:286)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:153)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Content is not allowed in prolog.
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:293)
at org.apache.ivy.core.retrieve.RetrieveEngine.determineArtifactsToCopy(RetrieveEngine.java:329)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:118)
... 7 more
Caused by: org.xml.sax.SAXParseException; systemId: file:/hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
at org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:328)
at org.apache.ivy.plugins.report.XmlReportParser$SaxXmlReportParser.parse(XmlReportParser.java:249)
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:291)
... 9 more
error: could not lock config file /hpc/users/willir31/.gitconfig: File exists
error: could not lock config file /hpc/users/willir31/.gitconfig: File exists
Dynamically requesting 1:1000 executors
Woops: /etc/hadoop/conf.cloudera.yarn/topology.py requires Python 2
Found $PYTHON2_HOME at /hpc/users/willir31/.local; attempting to prepend /hpc/users/willir31/.local/bin to $PATH...
Running command:
/hpc/users/willir31/c/adam/bin/adam-submit --master yarn --deploy-mode client --executor-cores 6 --executor-memory 17g --driver-memory 10g --conf spark.default.parallelism=1000 --conf spark.eventLog.enabled=true --conf spark.eventLog.dir=hdfs://demeter-nn1.demeter.hpc.mssm.edu:/spark/tmp/logs --conf spark.slim.host=hammerlab-dev3.hpc.mssm.edu --conf spark.extraListeners=org.apache.spark.JsonRelay --packages org.hammerlab:spark-json-relay:2.0.0 --conf spark.storage.memoryFraction=0.05 --conf spark.shuffle.memoryFraction=0.4 --conf spark.shuffle.service.enabled=true --conf spark.speculation=true --conf spark.speculation.interval=1000 --conf spark.speculation.multiplier=2 --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.minExecutors=1 --conf spark.dynamicAllocation.initialExecutors=1 --conf spark.dynamicAllocation.maxExecutors=1000 --conf spark.dynamicAllocation.schedulerBacklogTimeout=1 --conf spark.dynamicAllocation.executorIdleTimeout=300 --conf spark.yarn.executor.memoryOverhead=1024 --driver-java-options -Dyarn.resourcemanager.am.max-attempts=1 --conf spark.akka.timeout=120 --conf spark.file.transferTo=false --conf spark.core.connection.ack.wait.timeout=120 --conf spark.ui.enabled=false --executor-cores 10 --executor-memory 5g --driver-memory 1g --conf spark.shuffle.memoryFraction=0.8 -- transform /datasets/illumina_platinum/200x/fastq/ERR174369_1.fastq -paired_fastq /datasets/illumina_platinum/200x/fastq/ERR174369_2.fastq -concat /datasets/illumina_platinum/200x/fastq/ERR174369_unpaired.fastq -record_group ERR174369 -stringency SILENT /datasets/illumina_platinum/200x/ERR174369.adam
Using SPARK_SUBMIT=/hpc/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/bin/spark-submit
Ivy Default Cache set to: /hpc/users/willir31/.ivy2/cache
The jars for the packages stored in: /hpc/users/willir31/.ivy2/jars
:: loading settings :: url = jar:file:/demeter/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/lib/spark-assembly-1.5.0-hadoop2.6.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
org.hammerlab#spark-json-relay added as a dependency
:: resolving dependencies :: org.apache.spark#spark-submit-parent;1.0
confs: [default]
found org.hammerlab#spark-json-relay;2.0.0 in list
found org.json4s#json4s-jackson_2.10;3.2.10 in list
found org.json4s#json4s-core_2.10;3.2.10 in list
found org.json4s#json4s-ast_2.10;3.2.10 in list
found com.thoughtworks.paranamer#paranamer;2.6 in list
found com.fasterxml.jackson.core#jackson-databind;2.3.1 in list
found com.fasterxml.jackson.core#jackson-annotations;2.3.0 in list
found com.fasterxml.jackson.core#jackson-core;2.3.1 in list
found org.scala-lang#scalap;2.10.4 in list
found org.scala-lang#scala-compiler;2.10.4 in list
found org.scala-lang#scala-reflect;2.10.4 in list
:: resolution report :: resolve 2873ms :: artifacts dl 180ms
:: modules in use:
com.fasterxml.jackson.core#jackson-annotations;2.3.0 from list in [default]
com.fasterxml.jackson.core#jackson-core;2.3.1 from list in [default]
com.fasterxml.jackson.core#jackson-databind;2.3.1 from list in [default]
com.thoughtworks.paranamer#paranamer;2.6 from list in [default]
org.hammerlab#spark-json-relay;2.0.0 from list in [default]
org.json4s#json4s-ast_2.10;3.2.10 from list in [default]
org.json4s#json4s-core_2.10;3.2.10 from list in [default]
org.json4s#json4s-jackson_2.10;3.2.10 from list in [default]
org.scala-lang#scala-compiler;2.10.4 from list in [default]
org.scala-lang#scala-reflect;2.10.4 from list in [default]
org.scala-lang#scalap;2.10.4 from list in [default]
:: evicted modules:
org.scala-lang#scalap;2.10.0 by [org.scala-lang#scalap;2.10.4] in [default]
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 12 | 0 | 0 | 1 || 11 | 0 |
---------------------------------------------------------------------
:: problems summary ::
:::: ERRORS
unknown resolver null
unknown resolver null
:: USE VERBOSE OR DEBUG MESSAGE LEVEL FOR MORE DETAILS
:: retrieving :: org.apache.spark#spark-submit-parent
confs: [default]
Exception in thread "main" java.lang.RuntimeException: problem during retrieve of org.apache.spark#spark-submit-parent: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Premature end of file.
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:249)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:83)
at org.apache.ivy.Ivy.retrieve(Ivy.java:551)
at org.apache.spark.deploy.SparkSubmitUtils$.resolveMavenCoordinates(SparkSubmit.scala:1006)
at org.apache.spark.deploy.SparkSubmit$.prepareSubmitEnvironment(SparkSubmit.scala:286)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:153)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Premature end of file.
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:293)
at org.apache.ivy.core.retrieve.RetrieveEngine.determineArtifactsToCopy(RetrieveEngine.java:329)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:118)
... 7 more
Caused by: org.xml.sax.SAXParseException; Premature end of file.
at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:328)
at org.apache.ivy.plugins.report.XmlReportParser$SaxXmlReportParser.parse(XmlReportParser.java:249)
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:291)
... 9 more
ln: creating symbolic link `/hpc/users/willir31/s/yarn/ldl': File exists
ln: creating symbolic link `/hpc/users/willir31/s/yarn/ycl': File exists
ln: cannot remove `/hpc/users/willir31/s/yarn/yl': No such file or directory
ln: cannot remove `/hpc/users/willir31/s/yarn/yll': No such file or directory
Dynamically requesting 1:1000 executors
Woops: /etc/hadoop/conf.cloudera.yarn/topology.py requires Python 2
Found $PYTHON2_HOME at /hpc/users/willir31/.local; attempting to prepend /hpc/users/willir31/.local/bin to $PATH...
Running command:
/hpc/users/willir31/c/adam/bin/adam-submit --master yarn --deploy-mode client --executor-cores 6 --executor-memory 17g --driver-memory 10g --conf spark.default.parallelism=1000 --conf spark.eventLog.enabled=true --conf spark.eventLog.dir=hdfs://demeter-nn1.demeter.hpc.mssm.edu:/spark/tmp/logs --conf spark.slim.host=hammerlab-dev3.hpc.mssm.edu --conf spark.extraListeners=org.apache.spark.JsonRelay --packages org.hammerlab:spark-json-relay:2.0.0 --conf spark.storage.memoryFraction=0.05 --conf spark.shuffle.memoryFraction=0.4 --conf spark.shuffle.service.enabled=true --conf spark.speculation=true --conf spark.speculation.interval=1000 --conf spark.speculation.multiplier=2 --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.minExecutors=1 --conf spark.dynamicAllocation.initialExecutors=1 --conf spark.dynamicAllocation.maxExecutors=1000 --conf spark.dynamicAllocation.schedulerBacklogTimeout=1 --conf spark.dynamicAllocation.executorIdleTimeout=300 --conf spark.yarn.executor.memoryOverhead=1024 --driver-java-options -Dyarn.resourcemanager.am.max-attempts=1 --conf spark.akka.timeout=120 --conf spark.file.transferTo=false --conf spark.core.connection.ack.wait.timeout=120 --conf spark.ui.enabled=false --executor-cores 10 --executor-memory 5g --driver-memory 1g --conf spark.shuffle.memoryFraction=0.8 -- transform /datasets/illumina_platinum/200x/fastq/ERR174372_1.fastq -paired_fastq /datasets/illumina_platinum/200x/fastq/ERR174372_2.fastq -concat /datasets/illumina_platinum/200x/fastq/ERR174372_unpaired.fastq -record_group ERR174372 -stringency SILENT /datasets/illumina_platinum/200x/ERR174372.adam
Using SPARK_SUBMIT=/hpc/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/bin/spark-submit
Ivy Default Cache set to: /hpc/users/willir31/.ivy2/cache
The jars for the packages stored in: /hpc/users/willir31/.ivy2/jars
:: loading settings :: url = jar:file:/demeter/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/lib/spark-assembly-1.5.0-hadoop2.6.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
org.hammerlab#spark-json-relay added as a dependency
:: resolving dependencies :: org.apache.spark#spark-submit-parent;1.0
confs: [default]
found org.hammerlab#spark-json-relay;2.0.0 in list
found org.json4s#json4s-jackson_2.10;3.2.10 in list
found org.json4s#json4s-core_2.10;3.2.10 in list
found org.json4s#json4s-ast_2.10;3.2.10 in list
found com.thoughtworks.paranamer#paranamer;2.6 in list
found com.fasterxml.jackson.core#jackson-databind;2.3.1 in list
found com.fasterxml.jackson.core#jackson-annotations;2.3.0 in list
found com.fasterxml.jackson.core#jackson-core;2.3.1 in list
found org.scala-lang#scalap;2.10.4 in list
found org.scala-lang#scala-compiler;2.10.4 in list
found org.scala-lang#scala-reflect;2.10.4 in list
:: resolution report :: resolve 3123ms :: artifacts dl 76ms
:: modules in use:
com.fasterxml.jackson.core#jackson-annotations;2.3.0 from list in [default]
com.fasterxml.jackson.core#jackson-core;2.3.1 from list in [default]
com.fasterxml.jackson.core#jackson-databind;2.3.1 from list in [default]
com.thoughtworks.paranamer#paranamer;2.6 from list in [default]
org.hammerlab#spark-json-relay;2.0.0 from list in [default]
org.json4s#json4s-ast_2.10;3.2.10 from list in [default]
org.json4s#json4s-core_2.10;3.2.10 from list in [default]
org.json4s#json4s-jackson_2.10;3.2.10 from list in [default]
org.scala-lang#scala-compiler;2.10.4 from list in [default]
org.scala-lang#scala-reflect;2.10.4 from list in [default]
org.scala-lang#scalap;2.10.4 from list in [default]
:: evicted modules:
org.scala-lang#scalap;2.10.0 by [org.scala-lang#scalap;2.10.4] in [default]
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 12 | 0 | 0 | 1 || 11 | 0 |
---------------------------------------------------------------------
:: problems summary ::
:::: ERRORS
unknown resolver null
unknown resolver null
unknown resolver null
:: USE VERBOSE OR DEBUG MESSAGE LEVEL FOR MORE DETAILS
:: retrieving :: org.apache.spark#spark-submit-parent
confs: [default]
Exception in thread "main" java.lang.RuntimeException: problem during retrieve of org.apache.spark#spark-submit-parent: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Content is not allowed in prolog.
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:249)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:83)
at org.apache.ivy.Ivy.retrieve(Ivy.java:551)
at org.apache.spark.deploy.SparkSubmitUtils$.resolveMavenCoordinates(SparkSubmit.scala:1006)
at org.apache.spark.deploy.SparkSubmit$.prepareSubmitEnvironment(SparkSubmit.scala:286)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:153)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Content is not allowed in prolog.
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:293)
at org.apache.ivy.core.retrieve.RetrieveEngine.determineArtifactsToCopy(RetrieveEngine.java:329)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:118)
... 7 more
Caused by: org.xml.sax.SAXParseException; systemId: file:/hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
at org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:328)
at org.apache.ivy.plugins.report.XmlReportParser$SaxXmlReportParser.parse(XmlReportParser.java:249)
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:291)
... 9 more
ln: cannot remove `/hpc/users/willir31/s/yarn/ycl': No such file or directory
error: could not lock config file /hpc/users/willir31/.gitconfig: File exists
Dynamically requesting 1:1000 executors
Woops: /etc/hadoop/conf.cloudera.yarn/topology.py requires Python 2
Found $PYTHON2_HOME at /hpc/users/willir31/.local; attempting to prepend /hpc/users/willir31/.local/bin to $PATH...
Running command:
/hpc/users/willir31/c/adam/bin/adam-submit --master yarn --deploy-mode client --executor-cores 6 --executor-memory 17g --driver-memory 10g --conf spark.default.parallelism=1000 --conf spark.eventLog.enabled=true --conf spark.eventLog.dir=hdfs://demeter-nn1.demeter.hpc.mssm.edu:/spark/tmp/logs --conf spark.slim.host=hammerlab-dev3.hpc.mssm.edu --conf spark.extraListeners=org.apache.spark.JsonRelay --packages org.hammerlab:spark-json-relay:2.0.0 --conf spark.storage.memoryFraction=0.05 --conf spark.shuffle.memoryFraction=0.4 --conf spark.shuffle.service.enabled=true --conf spark.speculation=true --conf spark.speculation.interval=1000 --conf spark.speculation.multiplier=2 --conf spark.dynamicAllocation.enabled=true --conf spark.dynamicAllocation.minExecutors=1 --conf spark.dynamicAllocation.initialExecutors=1 --conf spark.dynamicAllocation.maxExecutors=1000 --conf spark.dynamicAllocation.schedulerBacklogTimeout=1 --conf spark.dynamicAllocation.executorIdleTimeout=300 --conf spark.yarn.executor.memoryOverhead=1024 --driver-java-options -Dyarn.resourcemanager.am.max-attempts=1 --conf spark.akka.timeout=120 --conf spark.file.transferTo=false --conf spark.core.connection.ack.wait.timeout=120 --conf spark.ui.enabled=false --executor-cores 10 --executor-memory 5g --driver-memory 1g --conf spark.shuffle.memoryFraction=0.8 -- transform /datasets/illumina_platinum/200x/fastq/ERR174377_1.fastq -paired_fastq /datasets/illumina_platinum/200x/fastq/ERR174377_2.fastq -concat /datasets/illumina_platinum/200x/fastq/ERR174377_unpaired.fastq -record_group ERR174377 -stringency SILENT /datasets/illumina_platinum/200x/ERR174377.adam
Using SPARK_SUBMIT=/hpc/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/bin/spark-submit
Ivy Default Cache set to: /hpc/users/willir31/.ivy2/cache
The jars for the packages stored in: /hpc/users/willir31/.ivy2/jars
:: loading settings :: url = jar:file:/demeter/users/willir31/sparks/spark-1.5.0-bin-hadoop2.6/lib/spark-assembly-1.5.0-hadoop2.6.0.jar!/org/apache/ivy/core/settings/ivysettings.xml
org.hammerlab#spark-json-relay added as a dependency
:: resolving dependencies :: org.apache.spark#spark-submit-parent;1.0
confs: [default]
found org.hammerlab#spark-json-relay;2.0.0 in list
found org.json4s#json4s-jackson_2.10;3.2.10 in list
found org.json4s#json4s-core_2.10;3.2.10 in list
found org.json4s#json4s-ast_2.10;3.2.10 in list
found com.thoughtworks.paranamer#paranamer;2.6 in list
found com.fasterxml.jackson.core#jackson-databind;2.3.1 in list
found com.fasterxml.jackson.core#jackson-annotations;2.3.0 in list
found com.fasterxml.jackson.core#jackson-core;2.3.1 in list
found org.scala-lang#scalap;2.10.4 in list
found org.scala-lang#scala-compiler;2.10.4 in list
found org.scala-lang#scala-reflect;2.10.4 in list
:: resolution report :: resolve 3240ms :: artifacts dl 131ms
:: modules in use:
com.fasterxml.jackson.core#jackson-annotations;2.3.0 from list in [default]
com.fasterxml.jackson.core#jackson-core;2.3.1 from list in [default]
com.fasterxml.jackson.core#jackson-databind;2.3.1 from list in [default]
com.thoughtworks.paranamer#paranamer;2.6 from list in [default]
org.hammerlab#spark-json-relay;2.0.0 from list in [default]
org.json4s#json4s-ast_2.10;3.2.10 from list in [default]
org.json4s#json4s-core_2.10;3.2.10 from list in [default]
org.json4s#json4s-jackson_2.10;3.2.10 from list in [default]
org.scala-lang#scala-compiler;2.10.4 from list in [default]
org.scala-lang#scala-reflect;2.10.4 from list in [default]
org.scala-lang#scalap;2.10.4 from list in [default]
:: evicted modules:
org.scala-lang#scalap;2.10.0 by [org.scala-lang#scalap;2.10.4] in [default]
---------------------------------------------------------------------
| | modules || artifacts |
| conf | number| search|dwnlded|evicted|| number|dwnlded|
---------------------------------------------------------------------
| default | 12 | 0 | 0 | 1 || 11 | 0 |
---------------------------------------------------------------------
:: retrieving :: org.apache.spark#spark-submit-parent
confs: [default]
Exception in thread "main" java.lang.RuntimeException: problem during retrieve of org.apache.spark#spark-submit-parent: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Content is not allowed in prolog.
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:249)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:83)
at org.apache.ivy.Ivy.retrieve(Ivy.java:551)
at org.apache.spark.deploy.SparkSubmitUtils$.resolveMavenCoordinates(SparkSubmit.scala:1006)
at org.apache.spark.deploy.SparkSubmit$.prepareSubmitEnvironment(SparkSubmit.scala:286)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:153)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:120)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
Caused by: java.text.ParseException: failed to parse report: /hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml: Content is not allowed in prolog.
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:293)
at org.apache.ivy.core.retrieve.RetrieveEngine.determineArtifactsToCopy(RetrieveEngine.java:329)
at org.apache.ivy.core.retrieve.RetrieveEngine.retrieve(RetrieveEngine.java:118)
... 7 more
Caused by: org.xml.sax.SAXParseException; systemId: file:/hpc/users/willir31/.ivy2/cache/org.apache.spark-spark-submit-parent-default.xml; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
at org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(SAXParser.java:328)
at org.apache.ivy.plugins.report.XmlReportParser$SaxXmlReportParser.parse(XmlReportParser.java:249)
at org.apache.ivy.plugins.report.XmlReportParser.parse(XmlReportParser.java:291)
... 9 more
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