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info on UL nanpore reads #267

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gambalab opened this issue Sep 18, 2023 · 2 comments
Open

info on UL nanpore reads #267

gambalab opened this issue Sep 18, 2023 · 2 comments

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@gambalab
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Hi,
If I use ultra long nanopore reads, are there any specific parameters I should use?

@jelber2
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jelber2 commented Sep 18, 2023

I do not think octopus was designed for this (not the Ultra-long part, rather the Nanopore part). Unless these are SUP-duplex reads, it does not have a high error rate long read preset. It does have some presets for low/moderate error rate PacBio Hifi (CCS) reads though.

@gambalab
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gambalab commented Sep 20, 2023

I tried for curiosity on several datasets and actually I always get this error at the end of the call

[2023-09-19 22:03:24] GL000214.1:129759 98.0% 1d 3h 32m 1s
[2023-09-19 22:07:38] KI270435.1:312 98.1% 1d 3h 30m 23s
[2023-09-19 22:13:39] KI270728.1:1872759 98.2% 1d 3h 28m 46s
[2023-09-19 22:16:29] KI270736.1:103786 98.3% 1d 3h 27m 6s
[2023-09-20 02:30:05] - 100% 1d 7h -
[2023-09-20 02:30:13] Starting Call Set Refinement (CSR) filtering
[2023-09-20 02:30:15] ------------------------------------------------------------------------
[2023-09-20 02:30:15] current | | time | estimated
[2023-09-20 02:30:15] position | completed | taken | ttc
[2023-09-20 02:30:15] ------------------------------------------------------------------------
terminate called after throwing an instance of 'octopus::hmm::HMMOverflow'
terminate called recursively
Aborted

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