SMRT View does not show reads in the details panel - pb-dyim/SMRT-Analysis GitHub Wiki

This troubleshooting page assumes you are able to open the SMRT View application itself, if not, please follow the steps in this article: SMRT View does not launch.

Step 1: Zoom in and turn on read view

Make sure you are zoomed in enough such that you can see the bases on the reference genome. Click on the "View Reads" icon located in the shortcuts bar at the top of the SMRT View Window.

Step 2: Check that your coverage is less than 100,000

SMRT View has a hard-cutoff of 100,000 reads to limit memory usage. Your computer or the server would freeze if this limit was not imposed. To make sure that you are not over the coverage limit, look at the coverage line plot in the "Regions Panel". Check the Y-axis to make sure it is not greater than 100,000

Step 3: Check for errors in the SMRT View Experience Index

Go to the SMRT Analysis home page at http://<your_hostname>:<your_port>/, and click on "SMRT View Home Page" --> "Experience Index". Note any errors that show up.

Step 3.1: If the error is as follows:

An error occurred reading data from test file: /mnt/ngswork/pacbio/smrtanalysis/common/test/jobs/scerevisiae/data/aligned_reads.cmp.h5
Your system may not be properly configured or some files required for reading HDF data are missing.

Check that HDF native library files are in $SEYMOUR_HOME/common/lib, e.g. libjhdf.so and libjhdf5.so for Linux, libjhdf.jnilib and libjhdf5.jnilib for Mac OS, jhdf.dll and jhdf5.dll for Windows.

Execute: ls $SEYMOUR_HOME/common/lib

Check that the script or command line argument used to start tomcat adds $SEYMOUR_HOME/common/lib to Java's native library path search, e.g. tomcatd includes -Djava.library.path=$SEYMOUR_HOME/common/lib

Execute: ps -ef | grep tomcat

Restart tomcat:

Execute: $SEYMOUR_HOME/etc/scripts/tomcatd restart