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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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Spades stucks at (chromosome_removal.cpp : 157) 76824 vertices left #1066

Open Ahmer1122 opened 1 year ago

Ahmer1122 commented 1 year ago

Description of bug

Spades get stucks at (chromosome_removal). Usually it take 5-10 minutes. However, it is stuck for more than 15 hours.

0:00:25.771 512M / 9G WARN General (chromosome_removal.cpp : 92) In most cases it means that either read coverage is uneven or significant contamination is present - both of these two cases make plasmidSPAdes' results unreliable 0:00:25.771 512M / 9G WARN General (chromosome_removal.cpp : 93) However, that situation may still be OK if you expect to see large plasmids in your dataset, so plasmidSPAdes will continue to work 0:00:25.930 520M / 9G INFO General (chromosome_removal.cpp : 102) Connected components calculated 0:00:25.969 520M / 9G INFO General (chromosome_removal.cpp : 121) Deleted 2 long edges 0:00:26.354 520M / 9G INFO General (chromosome_removal.cpp : 149) Before iteration 1 76824 vertices in graph 0:00:26.354 520M / 9G INFO General (chromosome_removal.cpp : 73) Removing of long chromosomal edges started 0:00:26.404 520M / 9G INFO General (chromosome_removal.cpp : 121) Deleted 0 long edges 0:00:26.418 520M / 9G INFO General (chromosome_removal.cpp : 151) Before dead_end simplification 0 76824 vertices in graph 0:00:26.785 520M / 9G INFO General (chromosome_removal.cpp : 156) Iteration 0 graph was not changed 0:00:26.785 520M / 9G INFO General (chromosome_removal.cpp : 157) 76824 vertices left

spades.log

spades.log

params.txt

params.txt

SPAdes version

SPAdes version: 3.13.1

Operating System

Linux ubuntu 20.04

Python Version

No response

Method of SPAdes installation

manual

No errors reported in spades.log

asl commented 1 year ago

Will you please give the latest SPAdes 3.15.5 a try? There were some fixes around

Ahmer1122 commented 1 year ago

I just tried it. But it stops at the same point.

asl commented 1 year ago

Tagging @Dmitry-Antipov

Dmitry-Antipov commented 1 year ago

According to the log, assembly is very fragmented - only 3280 bases in contigs longer than 1000bp (before chromosomal revomal stage), so there should not be reasonable output in any case.

However, it should not hang either. Can you share the data with us to reproduce this error?