Troubleshooting

General Troubleshooting Tips

Regardless of the platform, one can use the following environmental variables to better debug the workflow:

  • ADLB_DEBUG_RANKS=1 One can see if the processes are spread across the nodes correctly
  • TURBINE_LOG=1 Makes the Swift-T log output very verbose
  • TURBINE_LOG_FILE=<filePath> Changes the Swift-T log output from

StdOut to the file of choice

More debug info can be found here

FAQs

  • The pipeline seems to be running, but then prematurely stops at one of the tools?

    • Solution: make sure that all tools are specified in your runfile up to the executable itself (or the jar file if applicable)

  • The realignment/recalibration stage produces a lot of errors or strange results?

    • Solution: make sure you are preparing your reference and extra files (dbsnp, 1000G,…etc) according to the guidelines in the Data Preparation section

  • Things that should be running in parallel appear to be running sequencially

    • Solution: make sure you are setting the -n flag to a value at least one more than PROGRAMS_PER_NODE * NODES, as this allocates processes for Swift/T itself to run on
  • The job is killed as soon as BWA is called?
    • Solution: make sure there is no space in front of BWAMEMPARAMS
    • DO-THIS: BWAMEMPARAMS=-k 32 -I 300,30
    • NOT-THIS: BWAMEMPARAMS= -k 32 -I 300,30

  • I’m not sure how to run on a cluster that uses torque as a resource manager?

    • Clusters are typically configured to kill head node jobs that run longer than a few minutes, to prevent users from hogging the head node. Therefore, you may qsub the initial job, the swift-t command with its set variables, and it will qsub everybody else from its compute node.

  • I’m having difficulty running the plotting app. I get an error regarding plotly

    • The logging app depends on many R packages, including plotly and tidyverse. Some of these packages however require some OS specific packages. Fore deb systems (Debian, Ubuntu, ..etc), you may need to install libssl-dev, libcurl4-openssl-dev and libxml2-dev with your favourite package manager for tidyverse and plotly packages to work.