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Update run_eukphylo.sh

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Auden Cote-L'Heureux 2025-01-17 10:34:37 -05:00 committed by GitHub
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commit 2173eda5a0
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1 changed files with 2 additions and 2 deletions
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PTL2/run_eukphylo.sh
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@ -28,7 +28,7 @@ module load Python/3.9.6-GCCcore-11.2.0
export PATH=$PATH:/beegfs/fast/katzlab/grid_phylotol_setup/programs/standard-RAxML-master export PATH=$PATH:/beegfs/fast/katzlab/grid_phylotol_setup/programs/standard-RAxML-master
parent='/beegfs/fast/katzlab/' #add your path starting with the name of your folder, should begin with /beegfs/fast/katzlab/ parent='/beegfs/fast/katzlab/' #add your path starting with the name of your folder, should begin with /beegfs/fast/katzlab/
#if you are running batches, you need an srun line for each batch! #if you are running batches, you need an srun line for each batch!
srun --exact -n 1 -D ${parent} python3 ${parent}Scripts/phylotol.py --similarity_filter --sim_cutoff 0.95 --sim_taxa sim_taxa.txt --blacklist GuidanceRemovedSeqs_allConservedRuns_ML_nov_dec_2023.txt --start raw --end trees --gf_list B1_listofOGs.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}Output_folder_B1 > Output_folder_B1.out & srun --exact -n 1 -D ${parent} python3 ${parent}Scripts/eukphylo.py --similarity_filter --sim_cutoff 0.95 --sim_taxa sim_taxa.txt --blacklist GuidanceRemovedSeqs_allConservedRuns_ML_nov_dec_2023.txt --start raw --end trees --gf_list B1_listofOGs.txt --taxon_list taxon_list.txt --data OutgroupR2Gs --output ${parent}Output_folder_B1 > Output_folder_B1.out &
wait wait
###Grid end ###Grid end
@ -45,6 +45,6 @@ module load conda/latest
conda activate /work/pi_lkatz_smith_edu/Conda_PTL6p2/envs/PTL/ conda activate /work/pi_lkatz_smith_edu/Conda_PTL6p2/envs/PTL/
parent='/work/pi_lkatz_smith_edu/' #add your path startin> parent='/work/pi_lkatz_smith_edu/' #add your path startin>
#if you are running batches, you need an srun line for each batch! #if you are running batches, you need an srun line for each batch!
srun -D ${parent} python3 ${parent}Scripts/phylotol.py --similarity_filter --sim_cutoff 0.99 --> srun -D ${parent} python3 ${parent}Scripts/eukphylo.py --similarity_filter --sim_cutoff 0.99 -->
wait wait
###Unity end ###Unity end