Error : Hammar, Memmory allocation

[jojyjohn28]

Description of bug

I am trying to do the meta genome assembly through the SPAdes, but always ends up with error (after 3 days ). It is also taking days to complete the run.

I face two different errors, 1.the memory issue, PBS: job killed: mem 1572864112kb exceeded limit 1572864000kb (after 48 hours of running). So I continue from here and ends up with other error,

== Error == system call for: "['/zfs/gcl/software/gbf/SPAdes/3.15.5/bin/spades-hammer', '/zfs/camplab/Jojy/darpa_working/assembly_spades_results/body2_New_assembly_repeat/corrected/configs/config.info']" finished abnormally, OS return value: -9

Out of 8 meta genome, I could only complete 1. I tried both PBS and interactive jobs.

I am working on HPC of my University ,

qsub -I -q bigmem -l select=1:ncpus=40:mem=1500gb,walltime=160:00:00

Please help,

spades.log

spades.log

params.txt

params.txt

SPAdes version

3.15.5

Operating System

Linux-4.18.0-372.32.1.el8_6.x86_64-x86_64-with-glibc2.28

Python Version

3.9.7

Method of SPAdes installation

NA

No errors reported in spades.log

• [X] Yes