I am trying to run MAPS using Arima-MAPS_v2.0.sh, I've created the environment and samples are ready, however I am always encountering this error "Please provide an output folder (-O)!" despite I specify the path for the output, here is the sbatch I am running:
Hello,
I am trying to run MAPS using Arima-MAPS_v2.0.sh, I've created the environment and samples are ready, however I am always encountering this error "Please provide an output folder (-O)!" despite I specify the path for the output, here is the sbatch I am running:
Specify the path to the config file
config="/gpfs/data/HernandoLab/home/bericp01/Hi-ChIP_EN2_HOXD13/config.txt"
Extract sample_a name for the current $SLURM_ARRAY_TASK_ID
sample_a=$(awk -v ArrayTaskID=$SLURM_ARRAY_TASK_ID '$1==ArrayTaskID {print $3}' $config)
Extract sample_b name for the current $SLURM_ARRAY_TASK_ID
sample_b=$(awk -v ArrayTaskID=$SLURM_ARRAY_TASK_ID '$1==ArrayTaskID {print $4}' $config)
cd /gpfs/data/HernandoLab/home/bericp01/Hi-ChIP_EN2_HOXD13 mkdir outdir source /gpfs/data/HernandoLab/home/bericp01/bericp01_miniconda/etc/profile.d/conda.sh conda activate MAPS
outdir="/gpfs/data/HernandoLab/home/bericp01/Hi-ChIP_EN2_HOXD13/outdir/"
sh /gpfs/data/HernandoLab/home/bericp01/MAPS/bin/Arima-MAPS_v2.0.sh \ -C 1 \ -p broad \ -F 1 \ -M 1 \ -I ${sample_a} ${sample_b} \ -O outdir \ -o hg38 \ -b /gpfs/data/HernandoLab/home/bericp01/badal/GRCh38.primary_assembly.genome.fa \ -t 20 \ -f 1 \ -P 1 \ -H 1 \ -s 5000 \ -r 2000000 \ -d 2 \ -Q 30 \ -l 1000
I've also tried to use -O /gpfs/data/HernandoLab/home/bericp01/Hi-ChIP_EN2_HOXD13/config.txt
but again no success, someone has a clue about it?
Thanks Pietro