Dr. Kendall Lee

I am trying to rework it for slurm like this sbatch --mem=90 -pe smp 5 -l vf=2.5G -o /scratch/kcl58759/Eco_pacbio_kendall/Nextpolish_dir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh.o -e /scratch/kcl58759/Eco_pacbio_kendall/Nextpolish_dir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh.e /scratch/kcl58759/Eco_pacbio_kendall/Nextpolish_dir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh However, it keeps saying cant open smp. Is...

Hmm, I am confused about that. This is what happened when I tried the qsub command: The command was: '/opt/apps/slurm/21.08.5/bin/sbatch -e /scratch/kcl58759/Eco_pacbio_kendall/Nextpolish_dir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh.e -o /scratch/kcl58759/Eco_pacbio_kendall/Nextpolish_dir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh.o /scratch/kcl58759/Eco_pacbio_kendall/Nextpolish_dir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh 2>&1' and the output was:...

I believe I got this to work with: sbatch --partition=batch --ntasks=1 --cpus-per-task=5 --mem-per-cpu=537 --time=99:00:00 -o /scratch/kcl58759/Eco_pacbio_kendall/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh.o -e /scratch/kcl58759/Eco_pacbio_kendall/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh.e /scratch/kcl58759/Eco_pacbio_kendall/01_rundir/00.lgs_polish/01.db_split.sh.work/db_split1/nextPolish.sh However, I am unsure if there are further steps since I...

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...

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

If this helps, here is my log file and BUSCO output. [M::ha_analyze_count] lowest: count[5] = 3 [M::ha_analyze_count] highest: count[80] = 2280805 [M::ha_hist_line] 2: ****************************************************************************************************> 30448910 [M::ha_hist_line] 3: 62 [M::ha_hist_line] 4:...

The contig N50 I got using Quast is 5050728. I have attached the whole report as well! [1033.asm.report.pdf](https://github.com/chhylp123/hifiasm/files/7636670/1033.asm.report.pdf)

I am not sure what the het rate is. The species is presumed to be triploid Epichloe Coenophiala but potentially could be E. FatG-2/3/4 which are diploid. Regardless, the sample...