flagger
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mobinasri
Could not localize, doesn't exist
Hello, I get the following error when I try to run the flagger pipeline.
[2024-05-03 07:30:55,44] [error] BackgroundConfigAsyncJobExecutionActor [ddf63c0arunSecPhase.secphase:NA:1]: Error attempting to Execute
java.lang.Exception: Failed command instantiation
at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:674)
at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand$(StandardAsyncExecutionActor.scala:609)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand$lzycompute(ConfigAsyncJobExecutionActor.scala:200)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.instantiatedCommand(ConfigAsyncJobExecutionActor.scala:200)
at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents(StandardAsyncExecutionActor.scala:385)
at cromwell.backend.standard.StandardAsyncExecutionActor.commandScriptContents$(StandardAsyncExecutionActor.scala:384)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.commandScriptContents(ConfigAsyncJobExecutionActor.scala:200)
at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents(SharedFileSystemAsyncJobExecutionActor.scala:175)
at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.writeScriptContents$(SharedFileSystemAsyncJobExecutionActor.scala:174)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.cromwell$backend$sfs$BackgroundAsyncJobExecutionActor$$super$writeScriptContents(ConfigAsyncJobExecutionActor.scala:200)
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:200)
at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute(SharedFileSystemAsyncJobExecutionActor.scala:158)
at cromwell.backend.sfs.SharedFileSystemAsyncJobExecutionActor.execute$(SharedFileSystemAsyncJobExecutionActor.scala:155)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.execute(ConfigAsyncJobExecutionActor.scala:200)
at cromwell.backend.standard.StandardAsyncExecutionActor.$anonfun$executeAsync$1(StandardAsyncExecutionActor.scala:751)
at scala.util.Try$.apply(Try.scala:210)
at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync(StandardAsyncExecutionActor.scala:751)
at cromwell.backend.standard.StandardAsyncExecutionActor.executeAsync$(StandardAsyncExecutionActor.scala:751)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeAsync(ConfigAsyncJobExecutionActor.scala:200)
at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover(StandardAsyncExecutionActor.scala:1141)
at cromwell.backend.standard.StandardAsyncExecutionActor.executeOrRecover$(StandardAsyncExecutionActor.scala:1133)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.executeOrRecover(ConfigAsyncJobExecutionActor.scala:200)
at cromwell.backend.async.AsyncBackendJobExecutionActor.$anonfun$robustExecuteOrRecover$1(AsyncBackendJobExecutionActor.scala:65)
at cromwell.core.retry.Retry$.withRetry(Retry.scala:46)
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:270)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:270)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:270)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:270)
at akka.actor.Actor.aroundReceive(Actor.scala:539)
at akka.actor.Actor.aroundReceive$(Actor.scala:537)
at cromwell.backend.impl.sfs.config.BackgroundConfigAsyncJobExecutionActor.aroundReceive(ConfigAsyncJobExecutionActor.scala:200)
at akka.actor.ActorCell.receiveMessage(ActorCell.scala:614)
at akka.actor.ActorCell.invoke(ActorCell.scala:583)
at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:268)
at akka.dispatch.Mailbox.run(Mailbox.scala:229)
at akka.dispatch.Mailbox.exec(Mailbox.scala:241)
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 -> /scratch/rranallo-benavidez/flagger/BJ/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ:
doesn't exist
/scratch/rranallo-benavidez/flagger/BJ/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ -> /scratch/rranallo-benavidez/flagger/BJ: Operation not permitted
File not found /scratch/rranallo-benavidez/flagger/BJ/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/ca
ll-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/8
9f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp
/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/
call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase
/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-
2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/Fl
aggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/10
78326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/assembly.haplotype2.chm13v2.0.sorted.bam
Could not localize -> /scratch/rranallo-benavidez/flagger/BJ/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ:
doesn't exist
/scratch/rranallo-benavidez/flagger/BJ/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ -> /scratch/rranallo-benavidez/flagger/BJ: Operation not permitted
File not found /scratch/rranallo-benavidez/flagger/BJ/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/ca
ll-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/8
9f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp
/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/
call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase
/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-
2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/Fl
aggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/10
78326427/BJ.tmp/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/-519806452/BJ_hifi_all_vs_verkko_diploid_read_alignment.sorted_by_qname.bam
at common.validation.Validation$ValidationTry$.toTry$extension(Validation.scala:94)
at common.validation.Validation$ValidationTry$.toTry$extension(Validation.scala:90)
at cromwell.backend.standard.StandardAsyncExecutionActor.instantiatedCommand(StandardAsyncExecutionActor.scala:672)
... 44 common frames omitted
It mentions that
/scratch/rranallo-benavidez/flagger/BJ/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ
doesn't exist. However,
/scratch/rranallo-benavidez/flagger/BJ/cromwell-executions/FlaggerEndToEnd/89f0d04c-b9bd-45b8-a08b-2c6eb6756128/call-secphase/runSecPhase/ddf63c0a-d8d9-47f7-abf9-997ef218c6e1/call-secphase/inputs/1078326427/BJ.tmp
does exist.
Do you have any idea what might be causing this error? Thanks for any insights. Also, is there any reason why the file names are so nested? For example, the file not found seems to repeat the same folder structure multiple times.
@tbenavi1 Do you still have this issue? Could you please try Toil instead of cromwell for running WDLs? Here is the related link for running WDL with Toil: https://toil.readthedocs.io/en/latest/wdl/running.html
