How long and how much memory should NextPolish require?

[kcl58759]

Question or Expected behavior How long should it take for NextPolish to complete on a ~50Mb long read genome and what memory should I ask for? I submitted it at 90GB for 99hours and it timed out.

Operating system SLURM NextPolish/1.4.0-GCCcore-8.3.0-Python-3.8.2

GCC What version of GCC are you using? gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)

Python What version of Python are you using? You can use the command python --version to get it.Python 3.8.2

[moold]

Hi, depends on your input and parameters, but if you prefer to use your own alignment pipeline, it will cost less resources and be faster, here

[kcl58759]

Hi, I am trying to use my own alignment pipeline to decrease resources needed. Here is my alignment file:

!/bin/bash

SBATCH --job-name=NextPolishBWA

SBATCH --partition=batch

SBATCH --ntasks=5

SBATCH --cpus-per-task=10

SBATCH --mem=90gb

SBATCH --time=99:00:00

SBATCH --output=nextpolishself.out

SBATCH --error=nextpolishself.err

SBATCH --mail-user=kcl58759@uga.edu

SBATCH --mail-type=END,FAIL

module load BWA/0.7.17-GCC-8.3.0 ml SAMtools/1.10-GCC-8.3.0 ml NextPolish/1.4.0-GCCcore-8.3.0-Python-3.8.2

round=2 threads=20 read=/scratch/kcl58759/Eco_pacbio_kendall/pb_css_474/cromwell-executions/pb_ccs/c7a3dc30-7f94-40de-ac16-2445f965bfad/call-export_fasta/execution/m64060_210804_174320.hifi_reads.fasta.gz read_type=hifi mapping_option=["hifi"]="asm20" input=/scratch/kcl58759/Eco_pacbio_kendall/474.Primary.Hifi.asm/474.Primary.HiFi.asm.p_ctg.fa

for ((i=1; i<=2;i++)); do minimap2 -ax asm20 [hifi] -t 6 /scratch/kcl58759/Eco_pacbio_kendall/474.Primary.Hifi.asm/474.Primary.HiFi.asm.p_ctg.f /scratch/kcl58759/Eco_pacbio_kendall/pb_css_474/cromwell-executions/pb_ccs/c7a3dc30-7f94-40de-ac16-2445f965bfad/call-export_fasta/execution/m64060_210804_174320.hifi_reads.fasta.gz | samtools sort - -m 2g --threads 6 -o lgs.sort.bam; samtools index lgs.sort.bam; ls pwd/lgs.sort.bam > lgs.sort.bam.fofn; python NextPolish/lib/nextpolish2.py -g /scratch/kcl58759/Eco_pacbio_kendall/474.Primary.Hifi.asm/474.Primary.HiFi.asm.p_ctg.f-l lgs.sort.bam.fofn -r hifi -p 6 -sp -o genome.nextpolish.fa; if ((i!=2));then mv genome.nextpolish.fa genome.nextpolishtmp.fa; input=genome.nextpolishtmp.fa; fi; done;

However I keep getting the errors:

[ERROR] failed to open file '[hifi]': No such file or directory python: can't open file 'NextPolish/lib/nextpolish2.py': [Errno 20] Not a directory mv: cannot stat ‘genome.nextpolish.fa’: No such file or directory [ERROR] failed to open file '[hifi]': No such file or directory python: can't open file 'NextPolish/lib/nextpolish2.py': [Errno 20] Not a directory

Is there something I am missing?

[moold]

see minimap2 manual to checkout how to run minimap2, [hifi] is not a correct option.

[kcl58759]

I believe the issue is not with minimap but with NextPolish/lib/nextpolish2.py not being available. I cannot find the script on line and it doesn't load in with ml NextPolish/1.4.0-GCCcore-8.3.0-Python-3.8.2