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Plot bqsr error using wdl.

Hi there,

I keep getting hard link error during my plot_bqsr step using wdl.
Any suggestion how to fix it?
I tested the BQSR_1 and BQSR_2 both worked and on commandline I could run the AnalyzeCovariates step successfully.
Thanks!

`#Step6.1BQSR_1

call bqsr_1 {
input:
gatk=gatk,
inputBAM=markduplicate.dedupbam,
RefFasta=RefFasta,
knownSite1=dbsnp,
knownSite2=Mills_indels,
knownSite3=tenk_indels,
sampleName=sampleName,
Refdict=Refdict,
RefIndex=RefIndex,
bamindex=buildbamindex.bamindex
}

Step7.1BQSR_2

call bqsr_2 {
input:
gatk=gatk,
inputBAM=markduplicate.dedupbam,
RefFasta=RefFasta,
knownSite1=dbsnp,
knownSite2=Mills_indels,
knownSite3=tenk_indels,
sampleName=sampleName,
Refdict=Refdict,
RefIndex=RefIndex,
bamindex=buildbamindex.bamindex,
recaltable=bqsr_1.bqsr1table
}

Step8.plot_BQSR

call plot_bqsr {
input:
gatk=gatk,
RefFasta=RefFasta,
Refdict=Refdict,
RefIndex=RefIndex,
sampleName=sampleName,
recaltable=bqsr_1.bqsr1table,
postable=bqsr_2.bqsr2table
}
}

task plot_bqsr {
File gatk
File RefFasta
File recaltable
File postable
File sampleName
File Refdict
File RefIndex

command{
ln ${recaltable} b1.table
ln ${postable} b2.table
ln ${Refdict}

java -jar ${gatk} -T AnalyzeCovariates \
-R ${RefFasta} \
-before b1.table \
-after b2.table \
-plots ${sampleName}_recalibration_plots.pdf
}

output{
File recalibration_plot = "${sampleName}_recalibration_plots.pdf"
}

}

task bqsr_2{
File gatk
File inputBAM
String sampleName
File knownSite1
File knownSite2
File knownSite3
File RefFasta
File Refdict
File RefIndex
File bamindex
File recaltable

command{
ln ${inputBAM} input.bam
ln ${bamindex} input.bam.bai
ln ${Refdict}

java -jar ${gatk} -T BaseRecalibrator \
-R ${RefFasta} \
-I input.bam \
-knownSites ${knownSite1} \
-knownSites ${knownSite2} \
-knownSites ${knownSite3} \
-BQSR ${recaltable} \
-o ${sampleName}_post_recal_data.table
}

output{
File bqsr2table = "${sampleName}_post_recal_data.table"
}

}

task bqsr_1{
File gatk
File inputBAM
String sampleName
File knownSite1
File knownSite2
File knownSite3
File RefFasta
File Refdict
File RefIndex
File bamindex

command{
ln ${inputBAM} input.bam
ln ${bamindex} input.bam.bai
ln ${Refdict}

java -jar ${gatk} -T BaseRecalibrator \
-R ${RefFasta} \
-I input.bam \
-knownSites ${knownSite1} \
-knownSites ${knownSite2} \
-knownSites ${knownSite3} \
-o ${sampleName}_recal_data.table
}

output{
File bqsr1table = "${sampleName}_recal_data.table"
}

}`

{ "OUWES_test.Refsa": "/home/cytolab/Sand/Reference/ucsc.hg19.fasta.sa", "OUWES_test.picard": "/home/cytolab/Software/picard/picard.jar", "OUWES_test.gatk": "/home/cytolab/Software/GATK/GenomeAnalysisTK.jar", "OUWES_test.Refann": "/home/cytolab/Sand/Reference/ucsc.hg19.fasta.ann", "OUWES_test.inputBAML3R1": "/home/cytolab/Sand/testl3r1.fastq", "OUWES_test.inputBAML2R1": "/home/cytolab/Sand/testl2r1.fastq", "OUWES_test.dbsnp": "/home/cytolab/Sand/Reference/dbsnp_138.hg19.vcf", "OUWES_test.Mills_indels": "/home/cytolab/Sand/Reference/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf", "OUWES_test.tenk_indels": "/home/cytolab/Sand/Reference/1000G_phase1.snps.high_confidence.hg19.sites.vcf", "OUWES_test.Refdict": "/home/cytolab/Sand/Reference/ucsc.hg19.dict", "OUWES_test.RefFasta": "/home/cytolab/Sand/Reference/ucsc.hg19.fasta", "OUWES_test.RefIndex": "/home/cytolab/Sand/Reference/ucsc.hg19.fasta.fai", "OUWES_test.Refpac": "/home/cytolab/Sand/Reference/ucsc.hg19.fasta.pac", "OUWES_test.inputBAML1R2": "/home/cytolab/Sand/testl1r2.fastq", "OUWES_test.inputBAML1R1": "/home/cytolab/Sand/testl1r1.fastq", "OUWES_test.inputBAML2R2": "/home/cytolab/Sand/testl2r2.fastq", "OUWES_test.inputBAML4R1": "/home/cytolab/Sand/testl4r1.fastq", "OUWES_test.sampleName": "test769", "OUWES_test.Refbwt": "/home/cytolab/Sand/Reference/ucsc.hg19.fasta.bwt", "OUWES_test.inputBAML4R2": "/home/cytolab/Sand/testl4r2.fastq", "OUWES_test.inputBAML3R2": "/home/cytolab/Sand/testl3r2.fastq", "OUWES_test.Refamb": "/home/cytolab/Sand/Reference/ucsc.hg19.fasta.amb" }

calls: OUWES_test.plot_bqsr:NA:1
[2018-01-09 16:53:44,57] [warn] Localization via hard link has failed: /home/cytolab/Sand/cromwell-executions/OUWES_test/540ab5ba-34e3-4aaf-9992-0b891423e87f/call-plot_bqsr/inputs/home/cytolab/Sand/test769 -> /home/cytolab/Sand/test769
[2018-01-09 16:53:44,67] [warn] Couldn't find a suitable DSN, defaulting to a Noop one.
[2018-01-09 16:53:44,74] [info] Using noop to send events.
[2018-01-09 16:53:44,80] [warn] Localization via copy has failed: /home/cytolab/Sand/test769
[2018-01-09 16:53:44,93] [error] BackgroundConfigAsyncJobExecutionActor [540ab5baOUWES_test.plot_bqsr:NA:1]: Error attempting to Execute
cromwell.backend.standard.StandardAsyncExecutionActor$$anonfun$$nestedInanonfun$commandLinePreProcessor$1$1$$anon$1: :
Could not localize test769 -> /home/cytolab/Sand/cromwell-executions/OUWES_test/540ab5ba-34e3-4aaf-9992-0b891423e87f/call-plot_bqsr/inputs/home/cytolab/Sand/test769:
test769 doesn't exists
File not found /home/cytolab/Sand/cromwell-executions/OUWES_test/540ab5ba-34e3-4aaf-9992-0b891423e87f/call-plot_bqsr/inputs/home/cytolab/Sand/test769 -> /home/cytolab/Sand/test769
File not found test769
File not found /home/cytolab/Sand/test769
at cromwell.backend.standard.StandardAsyncExecutionActor$$anonfun$$nestedInanonfun$commandLinePreProcessor$1$1.applyOrElse(StandardAsyncExecutionActor.scala:113)
at cromwell.backend.standard.StandardAsyncExecutionActor$$anonfun$$nestedInanonfun$commandLinePreProcessor$1$1.applyOrElse(StandardAsyncExecutionActor.scala:112)
at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:34)
at scala.util.Failure.recoverWith(Try.scala:232)
at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$commandLinePreProcessor$1(StandardAsyncExecutionActor.scala:112)
at cromwell.backend.wdl.Command$.instantiate(Command.scala:27)
at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:207)
at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:206)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:121)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:121)
at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:177)
at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:176)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:121)
at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:136)
at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:135)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:121)
at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:11)
at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:10)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:121)
at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:123)
at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:121)
at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:254)
at scala.util.Try$.apply(Try.scala:209)
at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:254)
at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:254)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:121)
at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:510)
at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:504)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:121)
at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:56)
at cromwell.core.retry.Retry$.withRetry(Retry.scala:36)
at cromwell.backend.async.AsyncBackendJobExecutionActor.withRetry(AsyncBackendJobExecutionActor.scala:52)
at cromwell.backend.async.AsyncBackendJobExecutionActor.cromwell$backend$async$AsyncBackendJobExecutionActor$$robustExecuteOrRecover(AsyncBackendJobExecutionActor.scala:56)
at cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$receive$1.applyOrElse(AsyncBackendJobExecutionActor.scala:79)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
at akka.actor.Actor.aroundReceive(Actor.scala:513)
at akka.actor.Actor.aroundReceive$(Actor.scala:511)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.aroundReceive(ConfigAsyncJobExecutionActor.scala:121)
at akka.actor.ActorCell.receiveMessage(ActorCell.scala:527)
at akka.actor.ActorCell.invoke(ActorCell.scala:496)
at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:257)
at akka.dispatch.Mailbox.run(Mailbox.scala:224)
at akka.dispatch.Mailbox.exec(Mailbox.scala:234)
at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
[2018-01-09 16:53:45,13] [error] WorkflowManagerActor Workflow 540ab5ba-34e3-4aaf-9992-0b891423e87f failed (during ExecutingWorkflowState): :
Could not localize test769 -> /home/cytolab/Sand/cromwell-executions/OUWES_test/540ab5ba-34e3-4aaf-9992-0b891423e87f/call-plot_bqsr/inputs/home/cytolab/Sand/test769:
test769 doesn't exists
File not found /home/cytolab/Sand/cromwell-executions/OUWES_test/540ab5ba-34e3-4aaf-9992-0b891423e87f/call-plot_bqsr/inputs/home/cytolab/Sand/test769 -> /home/cytolab/Sand/test769
File not found test769
File not found /home/cytolab/Sand/test769
cromwell.backend.standard.StandardAsyncExecutionActor$$anonfun$$nestedInanonfun$commandLinePreProcessor$1$1$$anon$1: :
Could not localize test769 -> /home/cytolab/Sand/cromwell-executions/OUWES_test/540ab5ba-34e3-4aaf-9992-0b891423e87f/call-plot_bqsr/inputs/home/cytolab/Sand/test769:
test769 doesn't exists
File not found /home/cytolab/Sand/cromwell-executions/OUWES_test/540ab5ba-34e3-4aaf-9992-0b891423e87f/call-plot_bqsr/inputs/home/cytolab/Sand/test769 -> /home/cytolab/Sand/test769
File not found test769
File not found /home/cytolab/Sand/test769
at cromwell.backend.standard.StandardAsyncExecutionActor$$anonfun$$nestedInanonfun$commandLinePreProcessor$1$1.applyOrElse(StandardAsyncExecutionActor.scala:113)
at cromwell.backend.standard.StandardAsyncExecutionActor$$anonfun$$nestedInanonfun$commandLinePreProcessor$1$1.applyOrElse(StandardAsyncExecutionActor.scala:112)
at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:34)
at scala.util.Failure.recoverWith(Try.scala:232)
at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$commandLinePreProcessor$1(StandardAsyncExecutionActor.scala:112)
at cromwell.backend.wdl.Command$.instantiate(Command.scala:27)
at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:207)
at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:206)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:121)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:121)
at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:177)
at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:176)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:121)
at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:136)
at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:135)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:121)
at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:11)
at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:10)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:121)
at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:123)
at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:121)
at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:254)
at scala.util.Try$.apply(Try.scala:209)
at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:254)
at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:254)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:121)
at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:510)
at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:504)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:121)
at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:56)
at cromwell.core.retry.Retry$.withRetry(Retry.scala:36)
at cromwell.backend.async.AsyncBackendJobExecutionActor.withRetry(AsyncBackendJobExecutionActor.scala:52)
at cromwell.backend.async.AsyncBackendJobExecutionActor.cromwell$backend$async$AsyncBackendJobExecutionActor$$robustExecuteOrRecover(AsyncBackendJobExecutionActor.scala:56)
at cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$receive$1.applyOrElse(AsyncBackendJobExecutionActor.scala:79)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
at akka.actor.Actor.aroundReceive(Actor.scala:513)
at akka.actor.Actor.aroundReceive$(Actor.scala:511)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.aroundReceive(ConfigAsyncJobExecutionActor.scala:121)
at akka.actor.ActorCell.receiveMessage(ActorCell.scala:527)
at akka.actor.ActorCell.invoke(ActorCell.scala:496)
at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:257)
at akka.dispatch.Mailbox.run(Mailbox.scala:224)
at akka.dispatch.Mailbox.exec(Mailbox.scala:234)
at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)

[2018-01-09 16:53:45,13] [info] WorkflowManagerActor WorkflowActor-540ab5ba-34e3-4aaf-9992-0b891423e87f is in a terminal state: WorkflowFailedState
[2018-01-09 16:54:20,23] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
Workflow 540ab5ba-34e3-4aaf-9992-0b891423e87f transitioned to state Failed
[2018-01-09 16:54:20,46] [info] Automatic shutdown of the async connection
[2018-01-09 16:54:20,46] [info] Gracefully shutdown sentry threads.
[2018-01-09 16:54:20,46] [info] Shutdown finished.

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