Common Errors and How to Fix Them

1. My final_pruning or my sex4imputation and subset_ancestry rules have returned core dumps and segmentation faults. How do I fix this?

   These rules depend on OpenBLAS and need some variables to be set when running from a conda environment. Try running these options before resubmitting the command:

   export OMP_NUM_THREADS=1
   export USE_SIMPLE_THREADED_LEVEL3=1
   

2. The harmonize_hg38 step is failing due to lack of memory

   This happens due to system presets for java which is over-riding the memory that is needed for the job. Check what your $JAVA_OPTS are set them to a larger Xmx before restarting the pipeline. For example:

   JAVA_OPTS="-Xms256m -Xmx25g"
   

If you have any questions or issues, feel free to open an issue or directly email Drew Neavin (d.neavin @ garvan.org.au)