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Spades often gets stuck on read error correction #24

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bsiranosian opened this issue Jul 9, 2019 · 0 comments
Open

Spades often gets stuck on read error correction #24

bsiranosian opened this issue Jul 9, 2019 · 0 comments
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@bsiranosian
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bsiranosian commented Jul 9, 2019

This happens in about 5% of cases, looping away and wasting compute with no error. See ablab/spades#152

A solution is to split the read correction and assembler, and skip the read correction if it fails to compete after some reasonable amount of time.
spades-hammer can be run alone, then spades with the --only-assembler option

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