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marbl / verkko

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assertionerror insert_aln_gaps verkko v1.4.1 #217

Closed ptrebert closed 5 months ago

ptrebert commented 7 months ago

Hi,

I have one case (out of 60+) of the following assertion failing:

https://github.com/marbl/verkko/blob/6931eb3ba11cd3e07b4af61a286268baa48b965d/src/scripts/insert_aln_gaps.py#L221

Step 1a
10000
Step 2a
Traceback
[...]
assert path_length > current_left_clip + current_right_clip

This is with Verkko v1.4.1 and the previous releases of MBG and GraphAligner (1.0.15 and 1.0.17). I try reproducing the failure with the most recent releases of MBG and GraphAligner.

Best, Peter

skoren commented 6 months ago

Were you still seeing this crash with updated MBG/GraphAligner? Are these uploaded to globus?

ptrebert commented 6 months ago

The respective sample was updated with more HiFi data, causing a delay and the sample is thus still in the queue. I keep you posted.

ptrebert commented 5 months ago

Looks like the update of MBG/GraphAligner fixed that one