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Could not process output, file not found: /vlsci/SG0009/bshaban/gatk/development/cromwell-executions

Hi,

I am getting the error message below. This is occurring when I'm trying to save a file from the output for reuse in another task. If I don't reuse the outputs it provides no errors.

I've followed this example and I can't seem to get it to work. When i went through the tutorials, esp the the one with the simple haplotypecaller, I saw that the output file was copied to the working directory. In my example it doesn't seem that the output is copied from the input directory to the execution. I am very new to this so any help would be great! Thanks!

https://software.broadinstitute.org/wdl/documentation/plumbing#overview

my code is as follows

workflow rnaSeq {

        File inputFastqRead1
        File inputFastqRead2
        String threads
        String sampleName
        String genomeDir

        call fastqc {
            input:
                threads=threads,
                inputFastqRead1=inputFastqRead1,
                inputFastqRead2=inputFastqRead2,
                sampleName=sampleName
        }

        call star {
            input:
                threads=threads,
                genomeDir=genomeDir,
                inputFastqRead1=inputFastqRead1,
                inputFastqRead2=inputFastqRead2,
                sampleName=sampleName
        }
}

task fastqc {
        String threads
        File inputFastqRead1
        File inputFastqRead2
        String sampleName

        command {
                fastqc \
                        -t ${threads} \
                        ${inputFastqRead1} \
                        ${inputFastqRead2}
        }
        output {
                Array[File] results = glob("*html")
                File fastqR1 ="6h_1_fastqc.html"
                File fastqR2 ="6h_2_fastqc.html"
        }
}

task star {
        String threads
        String genomeDir
        String sampleName
        File inputFastqRead1
        File inputFastqRead2

        command {
                STAR --genomeDir ${genomeDir} \
                     --runThreadN ${threads} \
                     --readFilesIn ${inputFastqRead1} ${inputFastqRead2} \
                     --outFileNamePrefix ${sampleName}
        }
        output {
                Array[File] starResults = glob("*.sam")
                File starSam = "6hAligned.out.sam"
        }

}

[2018-01-12 00:40:12,51] [error] WorkflowManagerActor Workflow 574fdee5-bc01-483e-86d1-ddf0347a7f69 failed (during ExecutingWorkflowState): Could not process output, file not found: /vlsci/SG0009/bshaban/gatk/development/cromwell-executions/rnaSeq/574fdee5-bc01-483e-86d1-ddf0347a7f69/call-fastqc/execution/6h_1_fastqc.html
java.lang.RuntimeException: Could not process output, file not found: /vlsci/SG0009/bshaban/gatk/development/cromwell-executions/rnaSeq/574fdee5-bc01-483e-86d1-ddf0347a7f69/call-fastqc/execution/6h_1_fastqc.html
        at cromwell.backend.sfs.SharedFileSystem.mapJobWomFile(SharedFileSystem.scala:143)
        at cromwell.backend.sfs.SharedFileSystem.mapJobWomFile$(SharedFileSystem.scala:139)
        at cromwell.backend.sfs.SharedFileSystemJobCachingActorHelper$$anon$1.mapJobWomFile(SharedFileSystemJobCachingActorHelper.scala:13)
        at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.mapOutputWomFile(SharedFileSystemAsyncJobExecutionActor.scala:237)
        at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.mapOutputWomFile$(SharedFileSystemAsyncJobExecutionActor.scala:236)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.mapOutputWomFile(ConfigAsyncJobExecutionActor.scala:190)
        at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$outputValueMapper$1(StandardAsyncExecutionActor.scala:448)
        at wom.WomFileMapper$.$anonfun$mapWomFiles$1(WomFileMapper.scala:11)
        at scala.util.Try$.apply(Try.scala:209)
        at wom.WomFileMapper$.mapWomFiles(WomFileMapper.scala:11)
        at cromwell.backend.standard.StandardAsyncExecutionActor.outputValueMapper(StandardAsyncExecutionActor.scala:448)
        at cromwell.backend.standard.StandardAsyncExecutionActor.outputValueMapper$(StandardAsyncExecutionActor.scala:447)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.outputValueMapper(ConfigAsyncJobExecutionActor.scala:190)
        at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$evaluateOutputs$1(StandardAsyncExecutionActor.scala:465)
        at cromwell.backend.wdl.OutputEvaluator$.$anonfun$evaluateOutputs$5(OutputEvaluator.scala:65)
        at cats.data.EitherT.$anonfun$flatMap$1(EitherT.scala:80)
        at scala.util.Success.flatMap(Try.scala:247)
        at cats.instances.TryInstances$$anon$1.flatMap(try.scala:35)
        at cats.instances.TryInstances$$anon$1.flatMap(try.scala:14)
        at cats.data.EitherT.flatMap(EitherT.scala:78)
        at cromwell.backend.wdl.OutputEvaluator$.$anonfun$evaluateOutputs$4(OutputEvaluator.scala:64)
        at cats.data.EitherT.$anonfun$flatMap$1(EitherT.scala:80)
        at scala.util.Success.flatMap(Try.scala:247)
        at cats.instances.TryInstances$$anon$1.flatMap(try.scala:35)
        at cats.instances.TryInstances$$anon$1.flatMap(try.scala:14)
        at cats.data.EitherT.flatMap(EitherT.scala:78)
        at cromwell.backend.wdl.OutputEvaluator$.$anonfun$evaluateOutputs$1(OutputEvaluator.scala:63)
        at scala.util.Success.flatMap(Try.scala:247)
        at cromwell.backend.wdl.OutputEvaluator$.foldFunction$1(OutputEvaluator.scala:34)
        at cromwell.backend.wdl.OutputEvaluator$.$anonfun$evaluateOutputs$13(OutputEvaluator.scala:78)
        at scala.collection.LinearSeqOptimized.foldLeft(LinearSeqOptimized.scala:122)
        at scala.collection.LinearSeqOptimized.foldLeft$(LinearSeqOptimized.scala:118)
        at scala.collection.immutable.List.foldLeft(List.scala:86)
        at cromwell.backend.wdl.OutputEvaluator$.evaluateOutputs(OutputEvaluator.scala:78)
        at cromwell.backend.standard.StandardAsyncExecutionActor.evaluateOutputs(StandardAsyncExecutionActor.scala:465)
        at cromwell.backend.standard.StandardAsyncExecutionActor.evaluateOutputs$(StandardAsyncExecutionActor.scala:464)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.evaluateOutputs(ConfigAsyncJobExecutionActor.scala:190)
        at cromwell.backend.standard.StandardAsyncExecutionActor.handleExecutionSuccess(StandardAsyncExecutionActor.scala:517)
        at cromwell.backend.standard.StandardAsyncExecutionActor.handleExecutionSuccess$(StandardAsyncExecutionActor.scala:514)
        at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.handleExecutionSuccess(ConfigAsyncJobExecutionActor.scala:190)
        at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$handleExecutionResult$3(StandardAsyncExecutionActor.scala:718)
        at scala.concurrent.Future.$anonfun$flatMap$1(Future.scala:304)
        at scala.concurrent.impl.Promise.$anonfun$transformWith$1(Promise.scala:37)
        at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:60)
        at akka.dispatch.BatchingExecutor$AbstractBatch.processBatch(BatchingExecutor.scala:55)
        at akka.dispatch.BatchingExecutor$BlockableBatch.$anonfun$run$1(BatchingExecutor.scala:91)
        at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:12)
        at scala.concurrent.BlockContext$.withBlockContext(BlockContext.scala:81)
        at akka.dispatch.BatchingExecutor$BlockableBatch.run(BatchingExecutor.scala:91)
        at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
        at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:43)
        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)

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