made spongilla db, downloading reference databases

create_index.sh

+#!/bin/bash -ex
+#SBATCH -J create_index
+#SBATCH -t 02:00:00
+#SBATCH -c 12
+#SBATCH --mem=50G
+#SBATCH -o /g/arendt/npapadop/cluster/create_index.out
+#SBATCH -e /g/arendt/npapadop/cluster/create_index.err
+
+OUTPUT_DIR="$1"
+DATABASE="$2"
+
+cd ${OUTPUT_DIR}
+
+module load MMseqs2
+
+mmseqs createindex ${DATABASE} tmp --threads 12 --remove-tmp-files 1
+
+module unload MMseqs2
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databases.sh

+#!/bin/bash -ex
+#SBATCH -J databases
+#SBATCH -t 04:00:00
+#SBATCH -c 5
+#SBATCH --mem=50G
+#SBATCH -o /g/arendt/npapadop/cluster/databases2.out
+#SBATCH -e /g/arendt/npapadop/cluster/databases2.err
+
+DATABASE="$1"
+DATABASE_NAME="$2"
+OUTPUT_DIR="$3"
+
+cd ${OUTPUT_DIR}
+mkdir ${DATABASE_NAME}
+cd ${DATABASE_NAME}
+
+module load MMseqs2
+
+mmseqs databases ${DATABASE} ${DATABASE_NAME} tmp
+
+module unload MMseqs2
\ No newline at end of file

mkdb.sh

+#!/bin/bash -ex
+#SBATCH -J mkdb
+#SBATCH -t 10:00
+#SBATCH -c 1
+#SBATCH --mem=1G
+#SBATCH -o /g/arendt/npapadop/cluster/mkdb.out
+#SBATCH -e /g/arendt/npapadop/cluster/mkdb.err
+
+INPUT_PEP="$1"
+OUTPUT_DIR="$2"
+NAME="$3"
+
+mkdir ${OUTPUT_DIR}
+cd ${OUTPUT_DIR}
+
+module load MMseqs2
+
+mmseqs createdb ${INPUT_PEP} ${NAME}
+
+module unload MMseqs2
\ No newline at end of file

spongilla_create_index.sh

+#!/bin/bash -ex
+
+SCRIPT="/g/arendt/npapadop/repos/spongfold/create_index.sh"
+OUTPUT_DIR="/scratch/npapadop/Spongilla_lacustris_70AAcutoffTransDecoder/"
+DB_NAME="spongilla"
+
+sbatch ${SCRIPT} ${OUTPUT_DIR} ${DB_NAME}
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spongilla_mkdb.sh

+#!/bin/bash -ex
+
+SCRIPT="/g/arendt/npapadop/repos/spongfold/mkdb.sh"
+INPUT="/g/arendt/data/spongilla_singlecell_dataset/spongilla_lacustris_Trinity.fasta.transdecoder_70AA_mediumheader.pep"
+OUTPUT_DIR="/scratch/npapadop/Spongilla_lacustris_70AAcutoffTransDecoder/"
+DB_NAME="spongilla"
+
+sbatch ${SCRIPT} ${INPUT} ${OUTPUT_DIR} ${DB_NAME}
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