#!/bin/bash
# Grid Engine options (lines prefixed with #$)
#$ -N split_reads-3
#$ -cwd
#$ -l h_rt=00:10:00
#$ -l h_vmem=1G
#$ -P scs_speedup
#Array job :
#$ -t 1-1 #!!!!!!IMPORTANT: change to 1-num_of_samples


specie="human"
tag="only-CB-split"
## Variables declaration, change them to match your setup:
# File with all the sample IDs, one per line
idfile="/exports/eddie/scratch/$USER/Chimeras/Data/one-sample.txt"

# ## Running
# Assigning SAMPLE variable from the built-in array counter
sample=`sed -n ${SGE_TASK_ID}p "$idfile"`
echo "processing $sample"

# Change directory to the main project folder
cd /exports/eddie/scratch/$USER/Chimeras


#reads="outs/filter_70/reads/${tag}"
# now for test, use the previous one.
reads="outs/filter_70/reads/only-CB"

# split the file 
mkdir -p $reads/$sample
split -n 50 $reads/${sample}_${specie}_ids.txt $reads/$sample/${sample}_${specie}_ids.