repeat annotation

03-repeats/README.md

+# Repeat analysis
+
+Code in this folder covers the repeat analysis. It follows the production of a scaffolded draft
+genome (after juicebox).
+
+### Repeat prediction
+
+We modeled repeat families on the draft genome of _P. litorale_ using
+[RepeatModeler](prep-repeat-modeler.sh) and (soft-)masked them with
+[RepeatMasker](prep-repeat_masker.sh).
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03-repeats/prep-repeat-modeler.sh

+#!/usr/bin/env bash
+#
+#SBATCH --job-name=repeatmodeler_pycno
+#SBATCH --cpus-per-task=32
+#SBATCH --mem=20G
+#SBATCH --time=30:00:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=nikolaos.papadopoulos@univie.ac.at
+#SBATCH --output=/lisc/user/papadopoulos/log/pycno-repeats-%j.out
+#SBATCH --error=/lisc/user/papadopoulos/log/pycno-repeats-%j.err
+
+# will need optimisation from scratch when I next need it
+module load repeatmodeler/2.0.5-5.40.0-1.0.6
+# OLDDIR=/lisc/slurm/node-d02/tmp/slurm-9303351
+
+cd "$TMPDIR" || exit 1
+
+OUTDIR=/lisc/scratch/zoology/pycnogonum/genome/draft/repeats/repeat_modeller
+SCAFFOLDS=/lisc/scratch/zoology/pycnogonum/genome/draft/draft.fasta
+
+mkdir -p "$OUTDIR" || exit 1
+
+BuildDatabase -name pycno "$SCAFFOLDS"
+RepeatModeler -database pycno -threads 32 -LTRStruct > $OUTDIR/repeat_modeller_run.out
+
+# tar "$TMPDIR"/RM_*/ -czf "$OUTDIR"/repeatmodeler.tar.gz
+# cp "$TMPDIR"/run.out "$OUTDIR"/run.out
+
+# if the run was successful, there should be three result files:
+cp "$TMPDIR"/pycno-families.fa "$OUTDIR"/pycno-families.fa
+cp "$TMPDIR"/pycno-families.stk "$OUTDIR"/pycno-families.stk
+cp "$TMPDIR"/pycno-rmod.log "$OUTDIR"/pycno-rmod.log
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03-repeats/prep-repeat_masker.sh

+#!/usr/bin/env bash
+#
+#SBATCH --job-name=repeatmasker_pycno
+#SBATCH --cpus-per-task=4
+#SBATCH --mem=500M
+#SBATCH --time=4:00:00
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=nikolaos.papadopoulos@univie.ac.at
+#SBATCH --output=/lisc/user/papadopoulos/log/pycno-repeat-masker-%j.out
+#SBATCH --error=/lisc/user/papadopoulos/log/pycno-repeat-masker-%j.err
+
+# RepeatMasker is a lot less resource-intense than RepeatModeler, so it makes sense to run it as a separate script.
+# it ran out of memory with 500M, but it's unclear how much the last step needs
+module load repeatmasker/4.1.6-3.12.4-5.40.0
+
+SCAFFOLDS=/lisc/scratch/zoology/pycnogonum/genome/draft/draft.fasta
+OUTDIR=/lisc/scratch/zoology/pycnogonum/genome/draft/repeats/repeat_masker_gff
+mkdir -p "$OUTDIR" || exit 1
+
+cd "$OUTDIR" || exit 1
+FAMILIES="../repeat_modeller/pycno-families.fa"
+
+RepeatMasker -pa 4 -xsmall -gff -dir "$TMPDIR" -lib "$FAMILIES" "$SCAFFOLDS"
+
+# copy the results to the output directory:
+cp "$TMPDIR"/*.masked "$OUTDIR"/
+cp "$TMPDIR"/*.out "$OUTDIR"/
+cp "$TMPDIR"/*.tbl "$OUTDIR"/
+cp "$TMPDIR"/*.cat* "$OUTDIR"/
+cp "$TMPDIR"/*.gff "$OUTDIR"/
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