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Using spades --isolate option in circlator all #171

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brettmorg opened this issue Nov 2, 2020 · 0 comments
Open

Using spades --isolate option in circlator all #171

brettmorg opened this issue Nov 2, 2020 · 0 comments

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@brettmorg
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Hello, I'm trying to troubleshoot why my mitochondrial contig wasn't circularized, and in 03.assemble>warnings.log I found

* 0:00:03.219 15M / 74M WARN General (launcher.cpp : 172) Your data seems to have high uniform coverage depth. It is strongly recommended to use --isolate option.

Therefore I tried adding --assemble_spades_isolate, but get circlator: error: unrecognized arguments: --assemble_spades_isolate.

Is there a different way the isolate option should be added?

Best regards,
Brett
@brettmorg brettmorg changed the title Using spades --isolate option in circulator all Using spades --isolate option in circlator all Nov 2, 2020
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@brettmorg