#!/usr/bin/env bash
# Leave only one comment symbol on selected options
# Those with two commets will be ignored:
# The name to show in queue lists for this job:
##SBATCH -J pasa_fasq_STAR.sh

# Number of desired cpus (can be in any node):
##SBATCH --ntasks=1

# Number of desired cpus (all in same node):
#SBATCH --cpus=48

# Amount of RAM needed for this job:
#SBATCH --mem=500gb

# The time the job will be running:
#SBATCH --time=120:00:00

# To use GPUs you have to request them:
##SBATCH --gres=gpu:1

# If you need nodes with special features uncomment the desired constraint line:
# * to request only the machines with 80 cores and 2TB of RAM
##SBATCH --constraint=bigmem
# * to request only machines with 16 cores and 64GB with InfiniBand network
##SBATCH --constraint=cal
# * to request only machines with 24 cores and Gigabit network
##SBATCH --constraint=slim

# Set output and error files
#SBATCH --error=job.envia_STAR2_631052.sh.%J.err
#SBATCH --output=job.envia_STAR2_631052.sh.%J.out

# MAKE AN ARRAY JOB, SLURM_ARRAYID will take values from 1 to 100
##SARRAY --range=1-100

# To load some software (you can show the list with 'module avail'):
module load star/2.5.1b

export GENREF=/mnt/home/soft/human/data/hg38/hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips

# the program to execute with its parameters:

time STAR --runMode genomeGenerate --runThreadN 48 --outFileNamePrefix prefijo --genomeDir /mnt/home/soft/star/sample_scripts/genera_indice/ \
--limitGenomeGenerateRAM 500000000000 --genomeFastaFiles $GENREF/hg38.fa
#--readFilesIn hg38.fa
#time STAR --readFilesCommand zcat --runMode genomeGenerate --genomeFastaFiles hg19.fa --runThreadN 48 --outFileNamePrefix prefijo --genomeDir /mnt/home/soft/star/sample_scripts/genera_indice/ \
#--limitGenomeGenerateRAM 500000000000 --genomeFastaFiles $GENREF

echo `date` terminado

#!/usr/bin/env bash
# Leave only one comment symbol on selected options
# Those with two commets will be ignored:
# The name to show in queue lists for this job:
#SBATCH -J virsorter_jobname

# Number of desired cpus (can be in any node):
#SBATCH --ntasks=1

# Number of desired cpus (all in same node):
#SBATCH --cpus-per-task=8

# Amount of RAM needed for this job:
#SBATCH --mem=32gb

# The available nodes are:
# AMD nodes with 128 cores and 1800GB of usable RAM
# AMD nodes with 128 cores and 439GB of usable RAM
# Intel nodes with 52 cores and 187GB of usable RAM

# The time the job will be running:
#SBATCH --time=1:00:00

# If you need nodes with special features you can select a constraint.
# Please, use cal by default. You will be assigned a node that satisfies your requests.
#SBATCH --constraint=cal

# Change "cal" by "sd" if you want to use Intel nodes and by "sr" if you want to use AMD nodes.
##SBATCH --constraint=sd
##SBATCH --constraint=sr

# To use GPU, comment out the constraint line and uncomment the following line.
##SBATCH --gres=gpu:1

# Set output and error files
#SBATCH --error=job.%J.err
#SBATCH --output=job.%J.out

# Leave one comment in following line to make an array job. Then N jobs will be launched. In each one SLURM_ARRAY_TASK_ID will take one value from 1 to 100
##SBATCH --array=1-100

# To load some software (you can show the list with 'module avail'):
# module load software
module load virsorter/2.2.4
echo "Nodo: $(hostname)"
# the program to execute with its parameters:
time virsorter run -w test.out -i test.fa --min-length 1500 -j $SLURM_CPUS_PER_TASK all