Nextomics
How long and how much memory should NextPolish require?
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
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
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 [email protected] #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?
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