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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:
0
Demultiplexing
instead of:
3
(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.
The text was updated successfully, but these errors were encountered:
The bug aspect of this was fixed in #97 and the error parsing implemented in #104. The last step is to add a property summarizing current state (e.g. incomplete, errored, complete) and add it to the processor reporting.
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.The text was updated successfully, but these errors were encountered: