# module load singularity

scratch_dir=$(echo $PWD | sed 's/\/data\/ucct\/bi\/scratch_tmp/\/scratch/g')
mkdir log
echo "srun --chdir ${scratch_dir} --output logs/IQTREEMFP.%j.log --job-name IQTREEMFP --cpus-per-task 20 --mem 5G --partition short_idx --time 00:30:00 singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/iqtree:2.1.4_beta--hdcc8f71_0 iqtree -s ${scratch_dir}/../07-snphylo/snphylo.output.fasta -m MFP &" > _00_iqtreemfp.sh
echo "srun --chdir ${scratch_dir} --output logs/IQTREEFULLALIGN.%j.log --job-name IQTREEFULLALIGN --cpus-per-task 20 --mem 15G --partition short_idx --time 08:00:00 singularity exec -B ${scratch_dir}/../../../ /data/ucct/bi/pipelines/singularity-images/iqtree:2.1.4_beta--hdcc8f71_0 iqtree -s ${scratch_dir}/../07-snphylo/snphylo.output.fasta -m PMB+F+R2 -T 20 -B 1000 -pre phylo.iqtree.bootstrap &" > _01_iqtreeall.sh
