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SPAdes Genome Assembler
http://ablab.github.io/spades/
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[cloudspades-3.12.0-0]spades-core with K77 finished abnormally, err code: -8 #1143

Open ddzhang3 opened 1 year ago

ddzhang3 commented 1 year ago

Description of bug

I run the cloudspades with 10X genomics linked-reads for several samples. For some samples, the spade-core crashed with error code -8. I rerun the same sample with variable threads (--threads 20, 10) or variable memory (--memory 350), but nothing changed. Could you please give some advice?

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes-3.12.0-0

Operating System

Rocky Linux release 8.7 (Green Obsidian)

Python Version

Python 3.6.8

Method of SPAdes installation

conda

No errors reported in spades.log

Itolstoganov commented 1 year ago

Hi @ddzhang3, sorry for the late reply.

The crash is caused by the low number of edges longer than 5,000 in the SPAdes assembly graph. It seems that for this dataset cloudSPAdes will likely not be able to produce adequate scaffolds, since it relies on the long edges in the assembly graph, which are very few in this dataset.