spades-core finished abnormally, err code: 4

[GeorgeBGM]

Description of bug

Dear spades team,

• system call for: "['/home/users/ddu/anaconda3/pkgs/cloudspades-3.12.0-0/bin/spades-core', '/home/users/ddu/projects/009.RA/002.linked-reads/Assembly/Script/Cloudspades_HP1/K77/configs/config.info']" finished abnormally, err code: -8

Best, Du

spades.log

spades.log.zip

params.txt

params.txt.zip

SPAdes version

cloudspades-3.12.0

Operating System

linux

Python Version

Python 3.8.5

Method of SPAdes installation

conda

No errors reported in spades.log

• [X] Yes

[asl]

Tagging @Itolstoganov - cloudSPAdes author

[GeorgeBGM]

Dear spades team, Is there any progress on this issue or suggestions? Best, Du

[Itolstoganov]

Hi @George-du, sorry for the late reply.

The crash is caused by the absence of edges longer than 13500 in the SPAdes assembly graph. It is a bug that should be fixed in the near future. However, it seems that in this particular case cloudSPAdes will likely not be able to to anything, since it relies on the long edges in the assembly graph, which are very few in this dataset.

[GeorgeBGM]

Dear spades team,@Itolstoganov,

   Thanks for your helpful reply, I found that the error was reported for K77 and the rest of the smaller K values were fine, so would setting a smaller K-mer manually give the appropriate result?

Best, Du

[Itolstoganov]

Probably not. The edges are typically shorter on lower K, and the reason that there was no crash on the lower K values is that cloudSPAdes only runs during the last K.

[GeorgeBGM]

Dear spades team,@Itolstoganov, Thank you for your prompt and useful reply. Best, Du