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30 lines
1.8 KiB
Bash
30 lines
1.8 KiB
Bash
#!/bin/bash
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#
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#SBATCH --job-name=PTL1_GBF
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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/4.62.3-GCCcore-11.2.0
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module load Biopython/1.79-foss-2021b
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module load BLAST+/2.12.0-gompi-2021b
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module load DIAMOND/2.0.13-GCC-11.2.0
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module load VSEARCH/2.22.1-GCC-11.3.0
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parent='/beegfs/fast/katzlab/becky/PTL1/Transcriptomes/Forams/'
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srun -D ${parent}Scripts python3 ${parent}Scripts/wrapper.py -1 1 -2 7 -x --assembled_transcripts ${parent}AssembledTranscripts -o ${parent} -n ${parent}Conspecific.txt --genetic_code Universal &
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#srun -D ${parent}Scripts python3 ${parent}Scripts/wrapper.py -1 1 -2 7 -x --assembled_transcripts ${parent}Assembled_Transcripts -o ${parent} -n ${parent}Conspecific.txt --genetic_code ${parent}Gcodes.txt > log.out &
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#srun -D ${parent}HQ/Scripts python3 ${parent}HQ/Scripts/wrapper.py -1 2 -2 7 -x --assembled_transcripts ${parent}Plate7/Assembled_Transcripts -o ${parent}Plate7 -n ${parent}Plate7/Conspecific.txt --genetic_code ${parent}Plate7/Gcodes.txt &
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#srun -D ${parent}HQ/Scripts python3 ${parent}HQ/Scripts/wrapper.py -1 1 -2 7 -x --assembled_transcripts ${parent}Plate11/Assembled_Transcripts -o ${parent}Plate11 -n ${parent}Plate11/Conspecific.txt --genetic_code ${parent}Plate11/Gcodes.txt &
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#srun -D ${parent}HQ/Scripts python3 ${parent}HQ/Scripts/wrapper.py -1 2 -2 7 -x --assembled_transcripts ${parent}Plate18/Assembled_Transcripts -o ${parent}Plate18 -n ${parent}Plate18/Conspecific.txt --genetic_code ${parent}Plate18/Gcodes.txt &
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wait
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