Functional annotation pipeline failing when setting a path to a local copy of interproscan in uppmax about pipelines-nextflow

[mahesh-panchal]

If I understand your log snippet correctly, InterProScan is starting, but failing on something. You need to check the InterProScan log for what is failing.

Since the log will be on the scratch partition, it means you need to manually debug the error by running the script on a node.

Here's how:
Start an interactive session interactive -A <snic_account> -n <cores> -t <time>.
Go to the work directory /crex/proj/snic2020-2-19/private/horse_mackerel/data/00-genome/ensembl_early_release/work/work/29/b51e84025e1c38f0569102ff29bfdd and in there will be some hidden files with the scripts.
There are two scripts here of importance.
The .command.sh has the bash script. You can edit this to help with debugging, e.g. adding echo, or cat statements.
The .command.run script executes the .command.sh in the correct environment. If you look at this script, it will have the slurm directives at the top along with some complicated code for executing the .command.sh. Run the .command.run script using bash .command.run to run the Interproscan process directly on your interactive session (do not submit to slurm again). Also check where you scratch partition is echo $SNIC_TMP. When the process errors out again, find the Interproscan log on the $SNIC_TMP folder and see what the error is.

[apfuentes]

Here a snipped of the last lines of the error message printed in screen:

        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076)
        at java.base/java.lang.Thread.run(Thread.java:834)
  java.lang.IllegalStateException: Command line failed with exit code: 1
  Command: python3 bin/prosite/runprosite.py data/prosite/2021_01/profile_models /scratch/21458395/r278.uppmax.uu.se_20210802_122805023_3xnf//jobPrositeProfiles/000000000001_000000001000.fasta /scratch/21458395/r278.uppmax.uu.se_20210802_122805023_3xnf//jobPrositeProfiles/000000000001_000000001000.raw.out bin/prosite/pfsearchV3 -f -o 7 -t 4 
  Error output from binary:
  Error setting affinity!
  Error running prosite binary bin/prosite/pfsearchV3
  
        at uk.ac.ebi.interpro.scan.management.model.implementations.RunBinaryStep.execute(RunBinaryStep.java:201)
        at uk.ac.ebi.interpro.scan.jms.activemq.StepExecutionTransactionImpl.executeInTransaction(StepExecutionTransactionImpl.java:87)
        at jdk.internal.reflect.GeneratedMethodAccessor96.invoke(Unknown Source)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:343)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:198)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:163)
        at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:294)
        at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:98)
        at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:186)
        at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:212)
        at com.sun.proxy.$Proxy142.executeInTransaction(Unknown Source)
        at uk.ac.ebi.interpro.scan.jms.worker.LocalJobQueueListener.onMessage(LocalJobQueueListener.java:200)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doInvokeListener(AbstractMessageListenerContainer.java:761)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.invokeListener(AbstractMessageListenerContainer.java:699)
        at org.springframework.jms.listener.AbstractMessageListenerContainer.doExecuteListener(AbstractMessageListenerContainer.java:674)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.doReceiveAndExecute(AbstractPollingMessageListenerContainer.java:318)
        at org.springframework.jms.listener.AbstractPollingMessageListenerContainer.receiveAndExecute(AbstractPollingMessageListenerContainer.java:257)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.invokeListener(DefaultMessageListenerContainer.java:1189)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.executeOngoingLoop(DefaultMessageListenerContainer.java:1179)
        at org.springframework.jms.listener.DefaultMessageListenerContainer$AsyncMessageListenerInvoker.run(DefaultMessageListenerContainer.java:1076)
        at java.base/java.lang.Thread.run(Thread.java:834)
  java.lang.IllegalStateException: InterProScan exiting with non-zero status, see logs for further information.
        at uk.ac.ebi.interpro.scan.jms.activemq.NonZeroExitOnUnrecoverableError.failed(NonZeroExitOnUnrecoverableError.java:43)
        at uk.ac.ebi.interpro.scan.jms.master.StandaloneBlackBoxMaster.run(StandaloneBlackBoxMaster.java:167)
        at uk.ac.ebi.interpro.scan.jms.main.Run.main(Run.java:495)
  InterProScan analysis failed. Exception thrown by StandaloneBlackBoxMaster. Check the log file for details

Work dir:
  /crex/proj/snic2020-2-19/private/horse_mackerel/data/00-genome/ensembl_early_release/work/work/29/b51e84025e1c38f0569102ff29bfdd

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

[mahesh-panchal]

Were you able to find what the error was?

[mahesh-panchal]

Closing this. Feel free to reopen if you still have issues here.