Picked up _JAVA_OPTIONS: -Xms256M -Xmx16384M -XX:ParallelGCThreads=1
[2018-11-20 16:43:30,72] [info] Running with database db.url = jdbc:hsqldb:mem:e9c8a2c0-821e-477d-9ff6-c4d7efab5b97;shutdown=false;hsqldb.tx=mvcc
[2018-11-20 16:43:40,75] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
[2018-11-20 16:43:40,76] [info] [RenameWorkflowOptionsInMetadata] 100%
[2018-11-20 16:43:40,85] [info] Running with database db.url = jdbc:hsqldb:mem:3345e505-4bc1-47e2-9943-2426e7ae8c86;shutdown=false;hsqldb.tx=mvcc
[2018-11-20 16:43:41,18] [warn] This actor factory is deprecated. Please use cromwell.backend.google.pipelines.v1alpha2.PipelinesApiLifecycleActorFactory for PAPI v1 or cromwell.backend.google.pipelines.v2alpha1.PipelinesApiLifecycleActorFactory for PAPI v2
[2018-11-20 16:43:41,19] [warn] Couldn't find a suitable DSN, defaulting to a Noop one.
[2018-11-20 16:43:41,19] [info] Using noop to send events.
[2018-11-20 16:43:41,48] [info] Slf4jLogger started
[2018-11-20 16:43:41,76] [info] Workflow heartbeat configuration:
{
  "cromwellId" : "cromid-fbc48ab",
  "heartbeatInterval" : "2 minutes",
  "ttl" : "10 minutes",
  "writeBatchSize" : 10000,
  "writeThreshold" : 10000
}
[2018-11-20 16:43:41,80] [info] Metadata summary refreshing every 2 seconds.
[2018-11-20 16:43:41,84] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds.
[2018-11-20 16:43:41,84] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-11-20 16:43:41,84] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds.
[2018-11-20 16:43:42,86] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds.
[2018-11-20 16:43:42,88] [info] JES batch polling interval is 33333 milliseconds
[2018-11-20 16:43:42,88] [info] JES batch polling interval is 33333 milliseconds
[2018-11-20 16:43:42,88] [info] JES batch polling interval is 33333 milliseconds
[2018-11-20 16:43:42,89] [info] PAPIQueryManager Running with 3 workers
[2018-11-20 16:43:42,89] [info] SingleWorkflowRunnerActor: Version 34
[2018-11-20 16:43:42,90] [info] SingleWorkflowRunnerActor: Submitting workflow
[2018-11-20 16:43:42,96] [info] Unspecified type (Unspecified version) workflow 15fbfd45-15ec-4993-adbf-8676befc926b submitted
[2018-11-20 16:43:43,03] [info] SingleWorkflowRunnerActor: Workflow submitted 15fbfd45-15ec-4993-adbf-8676befc926b
[2018-11-20 16:43:43,04] [info] 1 new workflows fetched
[2018-11-20 16:43:43,04] [info] WorkflowManagerActor Starting workflow 15fbfd45-15ec-4993-adbf-8676befc926b
[2018-11-20 16:43:43,04] [warn] SingleWorkflowRunnerActor: received unexpected message: Done in state RunningSwraData
[2018-11-20 16:43:43,04] [info] WorkflowManagerActor Successfully started WorkflowActor-15fbfd45-15ec-4993-adbf-8676befc926b
[2018-11-20 16:43:43,04] [info] Retrieved 1 workflows from the WorkflowStoreActor
[2018-11-20 16:43:43,06] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes.
[2018-11-20 16:43:43,12] [info] MaterializeWorkflowDescriptorActor [15fbfd45]: Parsing workflow as WDL draft-2
[2018-11-20 16:43:55,59] [info] MaterializeWorkflowDescriptorActor [15fbfd45]: Call-to-Backend assignments: atac.ataqc -> Local, atac.bowtie2 -> Local, atac.macs2_ppr1 -> Local, atac.idr_pr -> Local, atac.pool_ta_pr2 -> Local, atac.macs2_ppr2 -> Local, atac.overlap -> Local, atac.bam2ta -> Local, atac.pool_ta_pr1 -> Local, atac.macs2_pr1 -> Local, atac.trim_adapter -> Local, atac.macs2_pr2 -> Local, atac.pool_ta -> Local, atac.read_genome_tsv -> Local, atac.xcor -> Local, atac.reproducibility_overlap -> Local, atac.reproducibility_idr -> Local, atac.idr_ppr -> Local, atac.macs2 -> Local, atac.filter -> Local, atac.spr -> Local, atac.overlap_ppr -> Local, atac.overlap_pr -> Local, atac.qc_report -> Local, atac.macs2_pooled -> Local, atac.idr -> Local
[2018-11-20 16:43:55,69] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,70] [warn] Local [15fbfd45]: Key/s [preemptible, disks, cpu, time, memory] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,70] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,70] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,70] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,70] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,70] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,70] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,70] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,70] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,70] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,70] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,70] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,71] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,71] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,71] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,71] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,71] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,71] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,71] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,71] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,71] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,71] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,71] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,71] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:55,71] [warn] Local [15fbfd45]: Key/s [cpu, memory, time, disks] is/are not supported by backend. Unsupported attributes will not be part of job executions.
[2018-11-20 16:43:58,04] [info] WorkflowExecutionActor-15fbfd45-15ec-4993-adbf-8676befc926b [15fbfd45]: Starting atac.read_genome_tsv
[2018-11-20 16:43:58,04] [info] WorkflowExecutionActor-15fbfd45-15ec-4993-adbf-8676befc926b [15fbfd45]: Condition met: '!true_rep_only'. Running conditional section
[2018-11-20 16:43:58,05] [info] WorkflowExecutionActor-15fbfd45-15ec-4993-adbf-8676befc926b [15fbfd45]: Condition met: 'enable_xcor'. Running conditional section
[2018-11-20 16:43:58,05] [info] WorkflowExecutionActor-15fbfd45-15ec-4993-adbf-8676befc926b [15fbfd45]: Condition met: 'enable_idr'. Running conditional section
[2018-11-20 16:43:58,05] [info] WorkflowExecutionActor-15fbfd45-15ec-4993-adbf-8676befc926b [15fbfd45]: Condition met: '!align_only && !true_rep_only && enable_idr'. Running conditional section
[2018-11-20 16:43:58,06] [info] WorkflowExecutionActor-15fbfd45-15ec-4993-adbf-8676befc926b [15fbfd45]: Condition met: '!align_only && !true_rep_only'. Running conditional section
[2018-11-20 16:43:58,06] [info] WorkflowExecutionActor-15fbfd45-15ec-4993-adbf-8676befc926b [15fbfd45]: Condition met: 'enable_idr'. Running conditional section
[2018-11-20 16:43:58,99] [warn] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.read_genome_tsv:NA:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-20 16:43:59,05] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
[2018-11-20 16:43:59,06] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
[2018-11-20 16:43:59,07] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.read_genome_tsv:NA:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.withRetry(AsyncBackendJobExecutionActor.scala:61)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.cromwell$backend$async$AsyncBackendJobExecutionActor$$robustExecuteOrRecover(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$receive$1.applyOrElse(AsyncBackendJobExecutionActor.scala:88)
	at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
	at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
	at akka.actor.Actor.aroundReceive(Actor.scala:517)
	at akka.actor.Actor.aroundReceive$(Actor.scala:515)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.aroundReceive(ConfigAsyncJobExecutionActor.scala:193)
	at akka.actor.ActorCell.receiveMessage(ActorCell.scala:588)
	at akka.actor.ActorCell.invoke(ActorCell.scala:557)
	at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:258)
	at akka.dispatch.Mailbox.run(Mailbox.scala:225)
	at akka.dispatch.Mailbox.exec(Mailbox.scala:235)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
Could not localize test_genome_database/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv:
	test_genome_database/hg38_local.tsv doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	File not found test_genome_database/hg38_local.tsv
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 42 common frames omitted
[2018-11-20 16:44:02,16] [info] WorkflowExecutionActor-15fbfd45-15ec-4993-adbf-8676befc926b [15fbfd45]: Starting atac.trim_adapter (2 shards)
[2018-11-20 16:44:02,89] [warn] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:0:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-20 16:44:02,89] [warn] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:1:1]: Unrecognized runtime attribute keys: disks, cpu, time, memory
[2018-11-20 16:44:02,91] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
[2018-11-20 16:44:02,91] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
[2018-11-20 16:44:02,92] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
[2018-11-20 16:44:02,92] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
[2018-11-20 16:44:02,92] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
[2018-11-20 16:44:02,92] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
[2018-11-20 16:44:02,92] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
[2018-11-20 16:44:02,92] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
[2018-11-20 16:44:02,92] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
[2018-11-20 16:44:02,92] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
[2018-11-20 16:44:02,92] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
[2018-11-20 16:44:02,93] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
[2018-11-20 16:44:02,93] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
[2018-11-20 16:44:02,93] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
[2018-11-20 16:44:02,93] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
[2018-11-20 16:44:02,93] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
[2018-11-20 16:44:02,93] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
[2018-11-20 16:44:02,93] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:0:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.withRetry(AsyncBackendJobExecutionActor.scala:61)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.cromwell$backend$async$AsyncBackendJobExecutionActor$$robustExecuteOrRecover(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$receive$1.applyOrElse(AsyncBackendJobExecutionActor.scala:88)
	at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
	at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
	at akka.actor.Actor.aroundReceive(Actor.scala:517)
	at akka.actor.Actor.aroundReceive$(Actor.scala:515)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.aroundReceive(ConfigAsyncJobExecutionActor.scala:193)
	at akka.actor.ActorCell.receiveMessage(ActorCell.scala:588)
	at akka.actor.ActorCell.invoke(ActorCell.scala:557)
	at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:258)
	at akka.dispatch.Mailbox.run(Mailbox.scala:225)
	at akka.dispatch.Mailbox.exec(Mailbox.scala:235)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 42 common frames omitted
[2018-11-20 16:44:02,93] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
[2018-11-20 16:44:02,94] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
[2018-11-20 16:44:02,94] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
[2018-11-20 16:44:02,94] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
[2018-11-20 16:44:02,94] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
[2018-11-20 16:44:02,95] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
[2018-11-20 16:44:02,95] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
[2018-11-20 16:44:02,95] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
[2018-11-20 16:44:02,95] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
[2018-11-20 16:44:02,95] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
[2018-11-20 16:44:02,96] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
[2018-11-20 16:44:02,96] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
[2018-11-20 16:44:02,96] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
[2018-11-20 16:44:02,96] [warn] Localization via hard link has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
[2018-11-20 16:44:02,98] [warn] Localization via copy has failed: /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
[2018-11-20 16:44:02,99] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:1:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.withRetry(AsyncBackendJobExecutionActor.scala:61)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.cromwell$backend$async$AsyncBackendJobExecutionActor$$robustExecuteOrRecover(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.backend.async.AsyncBackendJobExecutionActor$$anonfun$receive$1.applyOrElse(AsyncBackendJobExecutionActor.scala:88)
	at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
	at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
	at akka.actor.Actor.aroundReceive(Actor.scala:517)
	at akka.actor.Actor.aroundReceive$(Actor.scala:515)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.aroundReceive(ConfigAsyncJobExecutionActor.scala:193)
	at akka.actor.ActorCell.receiveMessage(ActorCell.scala:588)
	at akka.actor.ActorCell.invoke(ActorCell.scala:557)
	at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:258)
	at akka.dispatch.Mailbox.run(Mailbox.scala:225)
	at akka.dispatch.Mailbox.exec(Mailbox.scala:235)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 42 common frames omitted
[2018-11-20 16:44:03,36] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.read_genome_tsv:NA:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
	at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
	at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
	at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
Could not localize test_genome_database/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv:
	test_genome_database/hg38_local.tsv doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	File not found test_genome_database/hg38_local.tsv
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:04,67] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:1:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:05,20] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:0:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:05,30] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.read_genome_tsv:NA:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
Could not localize test_genome_database/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv:
	test_genome_database/hg38_local.tsv doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	File not found test_genome_database/hg38_local.tsv
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:08,73] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:1:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:09,74] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.read_genome_tsv:NA:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
Could not localize test_genome_database/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv:
	test_genome_database/hg38_local.tsv doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	File not found test_genome_database/hg38_local.tsv
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:09,79] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:0:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:12,03] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.read_genome_tsv:NA:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
Could not localize test_genome_database/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv:
	test_genome_database/hg38_local.tsv doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	File not found test_genome_database/hg38_local.tsv
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:12,46] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:0:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:13,44] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:1:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:17,43] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:1:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:18,37] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.read_genome_tsv:NA:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
Could not localize test_genome_database/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv:
	test_genome_database/hg38_local.tsv doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	File not found test_genome_database/hg38_local.tsv
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:18,38] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:0:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:19,67] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:1:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:22,53] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:0:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:22,90] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.read_genome_tsv:NA:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
Could not localize test_genome_database/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv:
	test_genome_database/hg38_local.tsv doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	File not found test_genome_database/hg38_local.tsv
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:23,54] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:1:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:26,42] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.read_genome_tsv:NA:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
Could not localize test_genome_database/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv:
	test_genome_database/hg38_local.tsv doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	File not found test_genome_database/hg38_local.tsv
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:27,26] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:1:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:28,63] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:0:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:31,61] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.read_genome_tsv:NA:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
	at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
	at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
	at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
Could not localize test_genome_database/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv:
	test_genome_database/hg38_local.tsv doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	File not found test_genome_database/hg38_local.tsv
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:32,91] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:0:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:34,34] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:1:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:37,71] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:0:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:40,39] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.read_genome_tsv:NA:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
	at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
	at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
	at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
Could not localize test_genome_database/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv:
	test_genome_database/hg38_local.tsv doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	File not found test_genome_database/hg38_local.tsv
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:42,12] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:1:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:42,52] [error] BackgroundConfigAsyncJobExecutionActor [15fbfd45atac.trim_adapter:0:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:40)
	at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:44)
	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)
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 common frames omitted
[2018-11-20 16:44:42,96] [error] WorkflowManagerActor Workflow 15fbfd45-15ec-4993-adbf-8676befc926b failed (during ExecutingWorkflowState): cromwell.core.CromwellFatalException: java.lang.Exception: Failed command instantiation
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.applyOrElse(Retry.scala:46)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.applyOrElse(Retry.scala:37)
	at scala.concurrent.Future.$anonfun$recoverWith$1(Future.scala:413)
	at scala.concurrent.impl.Promise.$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:44)
	at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
	at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
	at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
	at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Caused by: java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	... 6 more
Caused by: common.exception.AggregatedMessageException: Error(s):
:
Could not localize test_genome_database/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv:
	test_genome_database/hg38_local.tsv doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-read_genome_tsv/inputs/86352842/hg38_local.tsv -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	File not found test_genome_database/hg38_local.tsv
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_genome_database/hg38_local.tsv
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 more

cromwell.core.CromwellFatalException: java.lang.Exception: Failed command instantiation
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.applyOrElse(Retry.scala:46)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.applyOrElse(Retry.scala:37)
	at scala.concurrent.Future.$anonfun$recoverWith$1(Future.scala:413)
	at scala.concurrent.impl.Promise.$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:44)
	at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
	at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
	at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
	at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Caused by: java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	... 6 more
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF641SFZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF641SFZ.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF031ARQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF031ARQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF751XTV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF751XTV.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF590SYZ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF590SYZ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF927LSG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF927LSG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF734PEQ.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF734PEQ.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF859BDM.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF859BDM.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF007USV.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF007USV.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF193RRC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF193RRC.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF886FSC.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF886FSC.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031996/ENCFF366DFI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair1/ENCFF366DFI.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-1/inputs/1077031997/ENCFF573UXK.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep2/pair2/ENCFF573UXK.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 more

cromwell.core.CromwellFatalException: java.lang.Exception: Failed command instantiation
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.applyOrElse(Retry.scala:46)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.applyOrElse(Retry.scala:37)
	at scala.concurrent.Future.$anonfun$recoverWith$1(Future.scala:413)
	at scala.concurrent.impl.Promise.$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:44)
	at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
	at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
	at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
	at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
Caused by: java.lang.Exception: Failed command instantiation
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:537)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:472)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:301)
	at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:300)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:141)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:140)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents(BackgroundAsyncJobExecutionActor.scala:12)
	at cromwell.backend.sfs.BackgroundAsyncJobExecutionActor.writeScriptContents$(BackgroundAsyncJobExecutionActor.scala:11)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.writeScriptContents(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:124)
	at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:121)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:600)
	at scala.util.Try$.apply(Try.scala:209)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:600)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:915)
	at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:907)
	at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:193)
	at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
	at cromwell.core.retry.Retry$.withRetry(Retry.scala:37)
	at cromwell.core.retry.Retry$$anonfun$withRetry$1.$anonfun$applyOrElse$3(Retry.scala:44)
	at akka.pattern.FutureTimeoutSupport.liftedTree1$1(FutureTimeoutSupport.scala:26)
	at akka.pattern.FutureTimeoutSupport.$anonfun$after$1(FutureTimeoutSupport.scala:26)
	at akka.actor.Scheduler$$anon$4.run(Scheduler.scala:205)
	... 6 more
Caused by: common.exception.AggregatedMessageException: Error(s):
:
:
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF341MYG.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF248EJF.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz
	:
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528315/ENCFF106QGY.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz
	Could not localize test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz:
	test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz doesn't exist
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/cromwell-executions/atac/15fbfd45-15ec-4993-adbf-8676befc926b/call-trim_adapter/shard-0/inputs/189528316/ENCFF368TYI.subsampled.400.fastq.gz -> /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	File not found /netapp/home/kirsty.jamieson/dependencies/atac-seq-pipeline/test_sample/ENCSR356KRQ/fastq_subsampled/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz
	at common.validation.Validation$ValidationTry$.toTry$extension1(Validation.scala:72)
	at common.validation.Validation$ValidationTry$.toTry$extension0(Validation.scala:68)
	at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:535)
	... 35 more

[2018-11-20 16:44:42,97] [info] WorkflowManagerActor WorkflowActor-15fbfd45-15ec-4993-adbf-8676befc926b is in a terminal state: WorkflowFailedState
[2018-11-20 16:44:52,02] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
[2018-11-20 16:44:56,86] [info] Workflow polling stopped
[2018-11-20 16:44:56,87] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds
[2018-11-20 16:44:56,88] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds
[2018-11-20 16:44:56,88] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds
[2018-11-20 16:44:56,88] [info] Aborting all running workflows.
[2018-11-20 16:44:56,89] [info] JobExecutionTokenDispenser stopped
[2018-11-20 16:44:56,89] [info] WorkflowStoreActor stopped
[2018-11-20 16:44:56,89] [info] WorkflowLogCopyRouter stopped
[2018-11-20 16:44:56,89] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds
[2018-11-20 16:44:56,89] [info] WorkflowManagerActor All workflows finished
[2018-11-20 16:44:56,89] [info] WorkflowManagerActor stopped
[2018-11-20 16:44:56,89] [info] Connection pools shut down
[2018-11-20 16:44:56,89] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds
[2018-11-20 16:44:56,89] [info] Shutting down JobStoreActor - Timeout = 1800 seconds
[2018-11-20 16:44:56,89] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds
[2018-11-20 16:44:56,89] [info] SubWorkflowStoreActor stopped
[2018-11-20 16:44:56,89] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds
[2018-11-20 16:44:56,89] [info] Shutting down DockerHashActor - Timeout = 1800 seconds
[2018-11-20 16:44:56,89] [info] Shutting down IoProxy - Timeout = 1800 seconds
[2018-11-20 16:44:56,89] [info] CallCacheWriteActor Shutting down: 0 queued messages to process
[2018-11-20 16:44:56,89] [info] JobStoreActor stopped
[2018-11-20 16:44:56,89] [info] WriteMetadataActor Shutting down: 0 queued messages to process
[2018-11-20 16:44:56,89] [info] KvWriteActor Shutting down: 0 queued messages to process
[2018-11-20 16:44:56,89] [info] CallCacheWriteActor stopped
[2018-11-20 16:44:56,89] [info] DockerHashActor stopped
[2018-11-20 16:44:56,89] [info] IoProxy stopped
[2018-11-20 16:44:56,89] [info] ServiceRegistryActor stopped
[2018-11-20 16:44:56,92] [info] Database closed
[2018-11-20 16:44:56,92] [info] Stream materializer shut down
Workflow 15fbfd45-15ec-4993-adbf-8676befc926b transitioned to state Failed
[2018-11-20 16:44:56,95] [info] Automatic shutdown of the async connection
[2018-11-20 16:44:56,95] [info] Gracefully shutdown sentry threads.
[2018-11-20 16:44:56,96] [info] Shutdown finished.