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job.slurm
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/lustre/home/jydeng/mambaforge/bin/python NMF.py -i Fibroblast-slim.h5ad --method nndsvd --cell_type all -n 100 -k 4 -o "NMFk4-10"
/lustre/home/jydeng/mambaforge/bin/python NMF.py -i Fibroblast-slim.h5ad --method nndsvd --cell_type all -n 100 -k 5 -o "NMFk4-10"
/lustre/home/jydeng/mambaforge/bin/python NMF.py -i Fibroblast-slim.h5ad --method nndsvd --cell_type all -n 100 -k 6 -o "NMFk4-10"
/lustre/home/jydeng/mambaforge/bin/python NMF.py -i Fibroblast-slim.h5ad --method nndsvd --cell_type all -n 100 -k 7 -o "NMFk4-10"
/lustre/home/jydeng/mambaforge/bin/python NMF.py -i Fibroblast-slim.h5ad --method nndsvd --cell_type all -n 100 -k 8 -o "NMFk4-10"
/lustre/home/jydeng/mambaforge/bin/python NMF.py -i Fibroblast-slim.h5ad --method nndsvd --cell_type all -n 100 -k 9 -o "NMFk4-10"
/lustre/home/jydeng/mambaforge/bin/python NMF.py -i Fibroblast-slim.h5ad --method nndsvd --cell_type all -n 100 -k 10 -o "NMFk4-10"
#!/bin/bash
#SBATCH --job-name=[change]
#SBATCH --output=res.txt
#SBATCH --ntasks-per-node=8
#SBATCH --open-mode=append
#SBATCH --mail-user=damarisdeng@outlook.com
#SBATCH --mail-type=end
CURDIR=`pwd`
rm -rf $CURDIR/nodelist.$SLURM_JOB_ID
NODES=`scontrol show hostnames $SLURM_JOB_NODELIST`
for i in $NODES
do
echo "$i:$SLURM_NTASKS_PER_NODE" >> $CURDIR/nodelist.$SLURM_JOB_ID
done
echo $SLURM_NPROCS
echo "process will start at : "
date
echo "++++++++++++++++++++++++++++++++++++++++"
module load python
source /lustre/home/jydeng/mambaforge/etc/profile.d/conda.sh
conda activate base
# /lustre/home/jydeng/mambaforge/bin/python ../codes/s1_qc.py -p GSE205013
# echo "Finish running s1_qc.py"
# /lustre/home/jydeng/mambaforge/bin/python ../codes/s2_hvg.py -p d2_GSE205013_normlog -b patient
/lustre/home/jydeng/mambaforge/bin/python ../codes/s3_bbknn.py -p d3_GSE205013_hvg -b patient
/lustre/home/jydeng/mambaforge/bin/python ../codes/s8_cell_typist.py -i data
/lustre/home/jydeng/mambaforge/bin/python ../codes/s9_correlation.py -b "sample name" -i data_GSE183904 -s "Stage*" --levels Normal I II III IV DM --heatmap heatmap.csv
echo "++++++++++++++++++++++++++++++++++++++++"
echo "processs will sleep 30s"
sleep 30
echo "process end at : "
date
rm -rf $CURDIR/nodelist.$SLURM_JOB_ID