These are chat archives for nextflow-io/nextflow

27th
Apr 2019
Jonathan Manning
@pinin4fjords
Apr 27 09:29

Hi all! I'm running Nextflow from a shell script attached to a cron job, and email notifications are broken. Works fine called directly. The error complains about a carriage return:

javax.mail.MessagingException: Unable to send mail message
  mail exit status: 1
  reported error: foo@bar.ac.uk
 contains invalid character '\015'
Ignoring header field "Message-ID: <1156644651.0.1556356884476.JavaMail.foo@foo-bar.ac.uk>
"
Ignoring header field "MIME-Version: 1.0
"
Ignoring header field "Content-Type: text/plain; charset=UTF-8
"
Ignoring header field "Content-Transfer-Encoding: 7bit
"
No recipients specified
"/homes/foo/dead.letter" 37/1676

    at nextflow.mail.Mailer.sendViaSysMail(Mailer.groovy:261)
    at nextflow.mail.Mailer.send(Mailer.groovy:437)
    at nextflow.script.WorkflowNotifier.sendNotification(WorkflowNotifier.groovy:71)
    at nextflow.script.WorkflowMetadata.safeMailNotification(WorkflowMetadata.groovy:424)
    at nextflow.script.WorkflowMetadata.invokeOnComplete(WorkflowMetadata.groovy:377)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.base/java.lang.reflect.Method.invoke(Method.java:564)
    at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:101)
    at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1217)
    at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1041)
    at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1011)
    at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:994)
    at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:97)
    at nextflow.script.WorkflowMetadata$_closure3.doCall(WorkflowMetadata.groovy:233)
    at nextflow.script.WorkflowMetadata$_closure3.call(WorkflowMetadata.groovy)
    at nextflow.Session.shutdown0(Session.groovy:671)
    at nextflow.Session.destroy(Session.groovy:623)
    at nextflow.script.ScriptRunner.terminate(ScriptRunner.groovy:389)
    at nextflow.script.ScriptRunner.execute(ScriptRunner.groovy:172)
    at nextflow.cli.CmdRun.run(CmdRun.groovy:245)
    at nextflow.cli.Launcher.run(Launcher.groovy:449)
    at nextflow.cli.Launcher.main(Launcher.groovy:626)

Does anyone have an idea what's going on here?