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25 lines
862 B
Bash
25 lines
862 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 tqdm
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module load Biopython/1.75-foss-2019b-Python-3.7.4
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module load BLAST+/2.9.0-gompi-2019b
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module load DIAMOND/0.9.30-GCC-8.3.0
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path='/beegfs/fast/katzlab/PTL1/Genomes/'
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srun -D ${path}Scripts python3 ${path}Scripts/wrapper.py -1 1 -2 5 --cds ${path}PTL1GenomesBatches/PTL1GenomesBatch2 -o ${path}Output/PTL1Genomes_OutputBatch2 --genetic_code Universal --databases ${path}Databases &
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wait
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