SMRT® Portal job fails - pb-dyim/SMRT-Analysis GitHub Wiki

When a SMRT Portal job fails, you can troubleshoot the errors by looking at the $SEYMOUR_HOME/common/jobs/<job_id_prefix>/<job_id>/log/smrtpipe.log file.

Step 1. Examine the smrtportal log

If the job fails immediately, no job directory is created, and the smrtpipe.log file is never created, look for errors written to $SEYMOUR_HOME/common/log/smrtportal/smrtportal.0.log.

Step 2. Isolate software vs. data errors

If a smrtpipe.log file was created but you do not understand the error, you can try to isolate the problem to the software rather than the data by running the same protocol in SMRT Portal using the pre-packaged SMRT Cell in $SEYMOUR_HOME/common/test/primary/lambda, and the pre-packaged reference lambda sequence in $SEYMOUR_HOME/common/userdata/reference/lambda. If the lambda job also fails, then there is a problem with the software that must be investigated. Look in the smrtpipe.log file and continue.

Step 2. Get more verbose output

It is sometimes necessary to re-run the $SEYMOUR_HOME/common/jobs/<id_prefix>/<id>/job.sh script manually because the error messages in smrtpipe.log are not informative. To do this, add the --debug flag to the smrtpipe.py call in job.sh:

Create a minimal job_debug.sh for troubleshooting. Recall, the original job.sh should look like this:

. /opt/smrtanalysis/etc/setup.sh && export MPLCONFIGDIR=/opt/smrtanalysis/common/jobs/.matpl
otlib && ([[ ! -e $MPLCONFIGDIR ]] && mkdir $MPLCONFIGDIR ) || true && smrtpipe.py -D PROGRE
SS_URL=http://badger.nanofluidics.com:8080/smrtportal/api --distribute  --params=/opt/smrtan
alysis/common/jobs/016/016449/settings.xml --output=/opt/smrtanalysis/common/jobs/016/016449
 xml:/opt/smrtanalysis/common/jobs/016/016449/input.xml

The contents of job_debug.sh should look like this:

. /opt/smrtanalysis/etc/setup.sh smrtpipe.py --debug --params=settings.xml xml:input.xml

The main difference is that we get rid of extraneous arguments and full paths. Specifically, we removed the --distribute flag to rule out any cluster issues, and we added the --debug flag to get more verbose output in the smrtpipe.log file.

Step 3. Execute job_debug.sh within in the job directory

cd $SEYMOUR_HOME/common/jobs/<job_id_prefix>/<job_id>/
./job_debug.sh

Step 4. Report an issue

Highlight the error in the smrtpipe.log file and report your results from running a lambda control run.

Report an issue on github https://github.com/PacificBiosciences/SMRT-Analysis/issues

Report an issue on the customer portal if you have a PacBio RS: http://www.pacbioportal.com/