Error : Hammar, Memmory allocation
jojyjohn28 opened this issue · 0 comments
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
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
- Yes