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d59c79b149
These are PTL1 scripts from ACL on Feb8. NOTE: These are WITHOUT databases..... these are at (Katzlab only) link here https://drive.google.com/drive/folders/10n1GdTJqEOBg1nGA1hjxNHgaNZgmbwb5
23 lines
860 B
Bash
23 lines
860 B
Bash
#!/bin/bash
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#
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#SBATCH --job-name=PTL1_genome
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#SBATCH --output=PTL1.%j.out # Stdout (%j expands to jobId)
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#SBATCH --nodes=1
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#SBATCH --ntasks=1
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#SBATCH --ntasks-per-node=64 ##change to number of srun when running multiple instances
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#SBATCH --mem=160G
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#SBATCH --mail-type=ALL
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#SBATCH --mail-user=YOUREMAIL@smith.edu
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module purge #Cleans up any loaded modules
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module use /gridapps/modules/all #make sure module locations is loaded
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module load slurm
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module load Biopython/1.75-foss-2019b-Python-3.7.4
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module load BLAST+
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module load DIAMOND/0.9.30-GCC-8.3.0
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export PATH=$PATH:/Users/katzlab/scratch/katzlab/grid_phylotol_setup/programs/standard-RAxML-master
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export PATH=$PATH:/Users/katzlab/scratch/katzlab/grid_vsearch_setup/vsearch-2.15.1-linux-x86_64/bin
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python wrapper.py -1 1 -2 5 --cds ../TestData --genetic_code Universal --databases ../Databases |