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SegAlign crashes while running cactus on Terra #58

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hloucks opened this issue Oct 18, 2022 · 3 comments
Open

SegAlign crashes while running cactus on Terra #58

hloucks opened this issue Oct 18, 2022 · 3 comments

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@hloucks
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hloucks commented Oct 18, 2022

Glenn Hickey wanted me to report this issue I'm seeing while running ComparativeGenomicsToolkit/cactus on Terra. It looks like there is an issue in SegAlign causing the crash. I've attached the full log of errors I'm seeing when running.

Cactus_allerrors_20221014.txt
@glennhickey
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To further clarify: this is a crash in segalign_repeat_masker that happens on a 5.7Gb mollusk genome. run_segalign does seem to work on this genome, at least when aligning to human. It does not seem to be exceeding either system or video memory limits from my tests. We can share the genome on request.

@glennhickey glennhickey mentioned this issue Nov 7, 2022
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@gsneha26
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gsneha26 commented Nov 7, 2022

Can you share the genome files? I need to investigate the error outside of the container run logs.

@glennhickey
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I emailed a link to you.

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@glennhickey @gsneha26 @hloucks