ablab
Spades stucks at (chromosome_removal.cpp : 157) 76824 vertices left
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
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
- [X] Yes
Will you please give the latest SPAdes 3.15.5 a try? There were some fixes around
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?
