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alekseyzimin / masurca

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Polca.sh out of memory at samtools sort stage #188

Open Andrew-N-Black opened 4 years ago

Andrew-N-Black commented 4 years ago

Hello, I am trying to polish a pacbio assembly with illumina paired-end reads on a 1GB genome, but am running out of memory at the samtools sort stage. I am running on SLURM. Do you have any recommendations to prevent the job from getting killed and finishing? Thanks! -Andrew

polca.sh --version head (GNU coreutils) 8.22 Copyright (C) 2013 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html. This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law.

Written by David MacKenzie and Jim Meyering.

SLURM JOB:

SBATCH -t 14-00:00:00

SBATCH -n 40

SBATCH --mem=120G

cd $SLURM_SUBMIT_DIR

module load bioinfo module load bwa module load samtools module load boost/1.64.0

Usage: polca.sh -a -r <'Illumina_reads_fastq1 Illumina_reads_fastq'> -t [-n] [-m]

./polca.sh -a ../../pacbio/raw/Pupfish_Redbean_90X_arrow_2cells.fasta -r '040524_WP4-UM_S152_R1_filtered_val_1.fq.gz 040524_WP4-UM_S152_R2_filtered_val_2.fq.gz' -t 40 -m 5G

alekseyzimin commented 4 years ago

Please reduce the samtools memory parameter to 1G. The samtools memory is per thread, as described in the Usage message.