I get the following error when I enable call-caching in cromwell 30.1
2018-01-12 12:49:02,002 cromwell-system-akka.dispatchers.engine-dispatcher-57 ERROR - Failed to hash
java.io.IOException: Is a directory
at sun.nio.ch.FileDispatcherImpl.read0(Native Method)
at sun.nio.ch.FileDispatcherImpl.read(FileDispatcherImpl.java:46)
at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:223)
at sun.nio.ch.IOUtil.read(IOUtil.java:197)
at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:159)
at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65)
at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109)
at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103)
at org.apache.commons.codec.digest.DigestUtils.updateDigest(DigestUtils.java:794)
at org.apache.commons.codec.digest.DigestUtils.digest(DigestUtils.java:50)
at org.apache.commons.codec.digest.DigestUtils.md5(DigestUtils.java:274)
at org.apache.commons.codec.digest.DigestUtils.md5Hex(DigestUtils.java:310)
at cromwell.backend.impl.sfs.config.HashFileStrategy.$anonfun$hash$3(ConfigHashingStrategy.scala:82)
at cromwell.util.TryWithResource$.$anonfun$tryWithResource$1(TryWithResource.scala:16)
at scala.util.Try$.apply(Try.scala:209)
at cromwell.util.TryWithResource$.tryWithResource(TryWithResource.scala:10)
at cromwell.backend.impl.sfs.config.HashFileStrategy.hash(ConfigHashingStrategy.scala:82)
at cromwell.backend.impl.sfs.config.ConfigHashingStrategy.usingStandardInitData$1(ConfigHashingStrategy.scala:52)
at cromwell.backend.impl.sfs.config.ConfigHashingStrategy.getHash(ConfigHashingStrategy.scala:57)
at cromwell.backend.impl.sfs.config.ConfigBackendFileHashingActor.customHashStrategy(ConfigBackendFileHashingActor.scala:24)
at cromwell.backend.standard.callcaching.StandardFileHashingActor$$anonfun$fileHashingReceive$1.applyOrElse(StandardFileHashingActor.scala:70)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
at akka.actor.Actor.aroundReceive(Actor.scala:514)
at akka.actor.Actor.aroundReceive$(Actor.scala:512)
at cromwell.backend.standard.callcaching.StandardFileHashingActor.aroundReceive(StandardFileHashingActor.scala:57)
at akka.actor.ActorCell.receiveMessage(ActorCell.scala:527)
at akka.actor.ActorCell.invoke(ActorCell.scala:496)
at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:257)
at akka.dispatch.Mailbox.run(Mailbox.scala:224)
at akka.dispatch.Mailbox.exec(Mailbox.scala:234)
at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
2018-01-12 12:49:02,013 cromwell-system-akka.dispatchers.engine-dispatcher-72 ERROR - bec63d8d:complete.bwaaln:2:1: Hash error, disabling call caching for this job.
java.io.IOException: Is a directory
at sun.nio.ch.FileDispatcherImpl.read0(Native Method)
at sun.nio.ch.FileDispatcherImpl.read(FileDispatcherImpl.java:46)
at sun.nio.ch.IOUtil.readIntoNativeBuffer(IOUtil.java:223)
at sun.nio.ch.IOUtil.read(IOUtil.java:197)
at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:159)
at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:65)
at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:109)
at sun.nio.ch.ChannelInputStream.read(ChannelInputStream.java:103)
at org.apache.commons.codec.digest.DigestUtils.updateDigest(DigestUtils.java:794)
at org.apache.commons.codec.digest.DigestUtils.digest(DigestUtils.java:50)
at org.apache.commons.codec.digest.DigestUtils.md5(DigestUtils.java:274)
at org.apache.commons.codec.digest.DigestUtils.md5Hex(DigestUtils.java:310)
at cromwell.backend.impl.sfs.config.HashFileStrategy.$anonfun$hash$3(ConfigHashingStrategy.scala:82)
at cromwell.util.TryWithResource$.$anonfun$tryWithResource$1(TryWithResource.scala:16)
at scala.util.Try$.apply(Try.scala:209)
at cromwell.util.TryWithResource$.tryWithResource(TryWithResource.scala:10)
at cromwell.backend.impl.sfs.config.HashFileStrategy.hash(ConfigHashingStrategy.scala:82)
at cromwell.backend.impl.sfs.config.ConfigHashingStrategy.usingStandardInitData$1(ConfigHashingStrategy.scala:52)
at cromwell.backend.impl.sfs.config.ConfigHashingStrategy.getHash(ConfigHashingStrategy.scala:57)
at cromwell.backend.impl.sfs.config.ConfigBackendFileHashingActor.customHashStrategy(ConfigBackendFileHashingActor.scala:24)
at cromwell.backend.standard.callcaching.StandardFileHashingActor$$anonfun$fileHashingReceive$1.applyOrElse(StandardFileHashingActor.scala:70)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
at scala.PartialFunction$OrElse.applyOrElse(PartialFunction.scala:172)
at akka.actor.Actor.aroundReceive(Actor.scala:514)
at akka.actor.Actor.aroundReceive$(Actor.scala:512)
at cromwell.backend.standard.callcaching.StandardFileHashingActor.aroundReceive(StandardFileHashingActor.scala:57)
at akka.actor.ActorCell.receiveMessage(ActorCell.scala:527)
at akka.actor.ActorCell.invoke(ActorCell.scala:496)
at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:257)
at akka.dispatch.Mailbox.run(Mailbox.scala:224)
at akka.dispatch.Mailbox.exec(Mailbox.scala:234)
at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
It only happens in bwa align operations and only when I use hg19 reference (hg38 works fine).....
Using java version "1.8.0_151", cromwell 30.1.
Following is the cromwell config
include required(classpath("application"))
call-caching {
enabled = true
}
backend {
default = "Local"
providers {
Local {
actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
config {
run-in-background = true
submit = "/bin/bash ${script}"
concurrent-job-limit = 6
}
}
}
}
database {
profile = "slick.jdbc.MySQLProfile$"
db {
driver = "com.mysql.jdbc.Driver"
url = "jdbc:mysql://localhost/cromwell?useSSL=false&rewriteBatchedStatements=true"
user = "cg"
password = "*****"
connectionTimeout = 5000
}
}
workflow options
{
"workflow-failure-mode": "ContinueWhilePossible",
"write_to_cache": true,
"read_from_cache": true
}
relevant portion of inputs.json
"complete.reffasta": "/home/cg/resources/gatk/hg19/hg19ref.fa",
"complete.refindex": "/home/cg/resources/gatk/hg19/hg19ref.fa.fai",
"complete.refdict": "/home/cg/resources/gatk/hg19/hg19ref.dict",
"complete.bwaaln.refAmb": "/home/cg/resources/gatk/hg19/hg19ref.fa.amb",
"complete.bwaaln.refAnn": "/home/cg/resources/gatk/hg19/hg19ref.fa.ann",
"complete.bwaaln.refBwt": "/home/cg/resources/gatk/hg19/hg19ref.fa.bwt",
"complete.bwaaln.refPac": "/home/cg/resources/gatk/hg19/hg19ref.fa.pac",
"complete.bwaaln.refSa": "/home/cg/resources/gatk/hg19/hg19ref.fa.sa",
"complete.bwaaln.refAlt": "",
and relevant portion of wdl script
workflow complete {
File fastqPairsFile
Array[Array[String]] pairs = read_tsv(fastqPairsFile)
.....
scatter (pair in pairs) {
call bwaaln {
input:
name=name,
assembly=assembly,
bwa=bwa,
reffasta=reffasta,
refindex=refindex,
refdict=refdict,
pairID=pair[0],
id=pair[1],
sm=pair[2],
pl=pair[3],
lb=pair[4],
pu=pair[5],
reads1=pair[6],
reads2=pair[7]
}
....
task bwaaln {
File bwa
File reffasta
File refindex
File refdict
File? refAlt
File refAmb
File refAnn
File refBwt
File refPac
File refSa
String reads1
String reads2
String name
String id
String sm
String pl
String lb
String pu
String pairID
String assembly
command {
${bwa} mem -t 2 -M -R '@RG\tID:${id}\tSM:${sm}\tPL:${pl}\tLB:${lb}\tPU:${pu}' ${reffasta} ${reads1} ${reads2} > ${name}.${pairID}.${assembly}.bwa.aln.sam
}
output {
File outputsam = "${name}.${pairID}.${assembly}.bwa.aln.sam"
}
}
Thank you in advance for your time and effort.