Hello Terra Team,
I am running the CGA pipeline (CGA_WES_Characterization_Pipeline_v0.2_Jun2019) over a few pairs (~15 pairs). For each pair workflow runs scatter for MuTect1 and MuTect2 tasks. Workflow gets stuck on various shards for those two tasks. The most common step where workflow gets stuck is the localization of input files. It is accumulating cost while it is stuck.
We experienced the same issue during Christmas break and the cost of the running pipeline increased significantly because of that.
I am happy to share the workspace in order to figure out this problem.
I attached one screenshot for example for Call #11 that has been running for 3 hours but log file states that it is still localizing interval list file (which is a really small file)
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