Currently an alignment directory with incomplete output from a processing failure on the sequencer triggers a repeating "Alignment not recognized" error for the run, but that's only because the wrong ValueError is inadvertently caught. The Checkpoint.txt file for these cases is both an integer and a keyword (and the keyword gets included when trying to cast as int in umbra.illumna.util.load_checkpoint).
In these cases Checkpoint.txt looks like:
instead of:
(So there's an empty string in the usual case, and presumably other integers and keywords for the intermediates but I haven't seen them.)
Instead, load_checkpoint should be updated to get both the integer and the keyword, and any error entries in CompletedJobInfo.xml should be noted.
Currently an alignment directory with incomplete output from a processing failure on the sequencer triggers a repeating "Alignment not recognized" error for the run, but that's only because the wrong ValueError is inadvertently caught. The Checkpoint.txt file for these cases is both an integer and a keyword (and the keyword gets included when trying to cast as int in
umbra.illumna.util.load_checkpoint).In these cases Checkpoint.txt looks like:
instead of:
(So there's an empty string in the usual case, and presumably other integers and keywords for the intermediates but I haven't seen them.)
Instead,
load_checkpointshould be updated to get both the integer and the keyword, and any error entries in CompletedJobInfo.xml should be noted.