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Matt Post commented on JOSHUA-312: ---------------------------------- This is fixed with commit 301f301cdcad5ab49c8465506791e5f117e1c944 (just pushed). The problem was that I changed the structure of the alignment splits, and did not update the paths for Berkeley aligner. Sorry about the trouble! > Even though alignment is cached, it is always re-done in pipeline re-execution > ------------------------------------------------------------------------------ > > Key: JOSHUA-312 > URL: https://issues.apache.org/jira/browse/JOSHUA-312 > Project: Joshua > Issue Type: Improvement > Components: alignment > Affects Versions: 6.0.5 > Reporter: Lewis John McGibbney > Assignee: Lewis John McGibbney > Priority: Critical > Fix For: 6.2 > > > Say if a pipeline fails after alignment. The alignment result is never cached > and it becomes necessary to undertake alignment... again! > We should investigate the process for caching alignments as it would really > speed up rerunning end-to-end pipelines for large input datasets. -- This message was sent by Atlassian JIRA (v6.3.4#6332)