Smrt portal job status does not update - pb-dyim/SMRT-Analysis GitHub Wiki

SMRT Portal jobs are updated using a web services call. If the job fails to update it may appear to be stuck in "filtering" or "mapping" status on SMRT Portal, when the job is in fact completed according to the smrtpipe.log file.

Step 1: Check that the web services are alive.

Execute curl http://<hostname>:<port>/smrtportal/api. You should get the following response:

{
  "success" : true,
  "message" : "Web services are alive"
}

Try this command from the head node as well as any child nodes. Most update issues are due to hostname mapping problems. i.e. the child node does not recognize the head node using the hostname provided. You must examine your network configurations.

Step 2: Reset the hostname.

Execute $SEYMOUR_HOME/postinstall/configure_smrtanalysis.sh. When setting the hostname, you may want to consider the following:

the hostname needs to be recognized by any compute nodes
the hostname needs to be recognized by any external clients
the hostname should be immutable between reboots (static ip or dns recognized name)

Step 3: Verify the reported status of your job.

Execute curl http://<hostname>:<port>/smrtportal/api/jobs/<job_id>/status. You should get the following response:

{
  "jobStatusId" : 1856353,
  "jobId" : 56632,
  "code" : "Filtering",
  "jobStage" : null,
  "moduleName" : null,
  "percentComplete" : 100,
  "message" : "Successfully completed smrtpipe job",
  "name" : null,
  "whenCreated" : "2013-03-04T13:03:46-0800",
  "whenModified" : "2013-03-04T13:03:46-0800",
  "modifiedBy" : null,
  "createdBy" : "smrtpipe",
  "description" : null
}

Step 4: Reset the status to "Complete".

Execute curl -u <administrator>:<password> -d 'progress={"code":"Completed"}' http://<hostname>:8080/smrtportal/api/jobs/<job_id>/status. You should get the following response:

{
  "success" : true,
  "message" : "Job status updated"
}