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ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
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Error Code: -7 #154

Open juang0nzal3z opened 6 years ago

juang0nzal3z commented 6 years ago

I am assembling a two genomes independently with the following script:

spades.py -k 21,33,55,77,99,127 --careful -1 trim_SCLB_R1_paired.fq.gz -2 trim_SCLB_R2_paired.fq.gz -o spades_assembly

with the following job:

SBATCH --nodes=1 # Use one node

SBATCH --ntasks=1 # Run a single task

SBATCH --cpus-per-task=32 # Number of CPU cores per task

SBATCH --mem=64gb # Total memory limit

SBATCH --time=96:00:00 # Time limit hrs:min:sec

I get the following error message for both jobs: == Error == system call for: "['/apps/spades/3.12.0/bin/spades-hammer', 'spades_assembly/corrected/configs/config.info']" finished abnormally, err code: -7

1_params.txt 1_spades.log 2_params.txt 2_spades.log

asl commented 6 years ago

This looks like a memory issue. Does the problem reproduce with the restart or increased memory limit?

juang0nzal3z commented 6 years ago

Yes, I increased the memory from 32 to 64 gb and increased the number of threads to 32. The problem is the same and consistent for two different assemblies.

Does an assembly with 872881918 kmers require more memory?