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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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CoverageData::inc_coverage(int): Assertion `value >= 0 || coverage_ > unsigned(-value)' failed #1397

Closed wanghang7410 closed 1 month ago

wanghang7410 commented 1 month ago

Description of bug

Dear SPAdes developers,

Hello, I encountered an error while using SPAdes 4.0.0 for assembly. The error message is:

mimalloc: warning: unable to allocate aligned OS memory directly, fall back to over-allocation (5364514816 bytes, address: 0x7f3c10400000, alignment: 67108864, commit: 1) 0:25:51.958 18G / 19G INFO General (coverage_hash_map_builder.: 49) Collecting k-mer coverage information from reads, this takes a while. 0:27:55.333 18G / 19G INFO General (construction.cpp : 427) Filling coverage and flanking coverage from PHM spades-core: /__w/spades/spades/src/common/assembly_graph/core/debruijn_data.hpp:165: void debruijn_graph::CoverageData::inc_coverage(int): Assertionvalue >= 0 || coverage_ > unsigned(-value)' failed.

== Error == system call for: "['/SPAdes-4.0.0-Linux/bin/spades-core', '/home/flowhub/workdir/user_data/FLOWHUB_202400064/FLOWHUB_202400064_3/task/spades_4/NMD127/K21/configs/config.info']" finished abnormally, OS return value: -6 `

Could you please advise me on how to resolve this issue?

Thank you.

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPades v4.0.0

Operating System

Ubuntu 22.04.4

Python Version

3.10.12

Method of SPAdes installation

manual

No errors reported in spades.log

asl commented 1 month ago

You're likely having a k-mer with coverage more than 2 billion. I would suggest you to test for adapters and / or low-complexity sequences

wanghang7410 commented 1 month ago

This is very useful, thank you for your answer