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.

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