minion_pawsey

Process a metagenome through Rob's 2023 pipeline

This is the same scripts as in ../minion but I've "adapted" this to run on Pawsey. They are not optimised at all, but they run!

All commands in one go:

mkdir -p slurm_output/host_slurm  slurm_output/megahit_slurm  slurm_output/mmseqs_slurm  slurm_output/vamb_slurm slurm_output/fastp_slurm
find fastq -type f -printf "%f\n" > reads.txt

export NUM_R1_READS=$(wc -l reads.txt | cut -f 1 -d ' ')
SRC=~/atavide_lite/minion_pawsey

# download the databases
HUMANDLDJOB=$(sbatch --parsable $SRC/download_human.slurm)
MMSEQSDLD=$(sbatach --parsablle $SRC/mmseqs_download.slurm)

JOB=$(sbatch --parsable --array=1-$NUM_R1_READS:1 $SRC/fastp.slurm)
HOSTJOB=$(sbatch --parsable --array=1-$NUM_R1_READS:1 --dependency=afterok:$JOB,$HUMANDLDJOB $SRC/host_removal.slurm)
FAJOB=$(sbatch --parsable --dependency=afterok:$HOSTJOB $SRC/fastq2fasta.slurm)
MMSEQSJOB=$(sbatch --parsable --array=1-$NUM_R1_READS:1 --dependency=afterok:$FAJOB,$MMSEQSDLD $SRC/mmseqs_easy_taxonomy.slurm)
sbatch --dependency=afterok:$MMSEQSJOB $SRC/mmseqs_taxonomy.slurm
sbatch --dependency=afterok:$MMSEQSJOB $SRC/read_fate.slurm
SSJOB=$(sbatch --parsable --dependency=afterok:$MMSEQSJOB --array=1-$NUM_R1_READS:1 $SRC/mmseqs_add_subsystems_taxonomy.slurm)
sbatch --dependency=afterok:$SSJOB $SRC/count_subsystems.slurm
MEGAHITJOB=$(sbatch  --parsable --dependency=afterok:$HOSTJOB --array=1-$NUM_R1_READS:1 $SRC/megahit.slurm)
VCJOB=$(sbatch --parsable --dependency=afterok:$MEGAHITJOB $SRC/vamb_concat.slurm)
VMJOB=$(sbatch --parsable  --dependency=afterok:$VCJOB --array=1-$NUM_R1_READS:1 $SRC/vamb_minimap.slurm)
VAMBJOB=$(sbatch --parsable --dependency=afterany:$VMJOB $SRC/vamb.slurm)
CHECKMJOB=$(sbatch --parsable --dependency=afterany:$VAMBJOB $SRC/checkm.slurm vamb/bins/ vamb/checkm)