File size: 2,717 Bytes
80a72c3 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 | #!/bin/bash
#These are optional flags but you probably want them in all jobs
#$ -S /bin/bash
#$ -j y
#
# Submit chainsaw job array to SGE cluster
#
# usage:
# qsub -t 1-16933 chainsaw_submit.ucl_cs.sh
#
# Assumes index file has been split into chunks e.g. "zipindex.00000001":
# split -a 8 -d 1 -l 1000 data/zipindex zipindex.
#
if [[ "$SGE_TASK_ID" == "undefined" ]]; then
echo "Need to specify the job array details in the qsub command"
echo "example: qsub -t 1-16933:1 <script>"
echo
exit 1
fi
CATH_VERSION=v4_3_0
ZIP_DIR=/SAN/bioinf/afdb_domain/zipfiles
HOME_DIR=/home/$USER
SHARED_REPO=/SAN/cath/cath_v4_3_0/alphafold/chainsaw_on_alphafold/chainsaw
SHARED_REPO="${SHARED_REPO:-${SGE_O_WORKDIR}/chainsaw}"
ZIP_EXTRACT=$SHARED_REPO/scripts/zip_extract.py
SCRATCH_DIR=/scratch0/$USER
LOCAL_TASK_DIR=$SCRATCH_DIR/$JOB_NAME-$JOB_ID-$SGE_TASK_ID
PYTHON_EXE=${SGE_O_WORKDIR}/venv/bin/python3
# assumes the zip index file has been split into chunks (named 'zipindex.00000001')
ZIP_INDEX_FILE=/SAN/bioinf/afdb_domain/datasets/index/all_models_unique_partitions/zip_index.$(printf "%08d" $SGE_TASK_ID)
RESULTS_FILE=${SGE_O_WORKDIR}/results/$(basename $ZIP_INDEX_FILE).results.csv
if [ ! -e "${PYTHON_EXE}" ]
then
echo "ERROR: python executable does not exist - have you built a venv? (PYTHON_EXE=$PYTHON_EXE)"
exit 1
fi
if [ ! -e "${ZIP_INDEX_FILE}" ]
then
echo "ERROR: input index file '${ZIP_INDEX_FILE}' does not exist"
exit 1
fi
if [ -e "${RESULTS_FILE}" ]
then
echo "ERROR: output file '${RESULTS_FILE}' already exists (will not overwrite)"
exit 1
fi
echo "INDEX_FILE : $ZIP_INDEX_FILE"
echo "RESULTS_FILE : $RESULTS_FILE"
echo "DATE_STARTED : "`date`
echo
echo "HOSTNAME : $HOSTNAME"
echo "SGE_TASK_ID : $SGE_TASK_ID"
echo "GIT_REMOTE : $SHARED_REPO"
echo "LOCAL_TASK_DIR : $LOCAL_TASK_DIR"
# die on error
set -o errexit
echo "Creating output directories ..."
mkdir -p $LOCAL_TASK_DIR
mkdir -p $(dirname $RESULTS_FILE)
echo "...DONE"
echo "Loading python ..."
source /share/apps/source_files/python/python-3.8.5.source
# source ./venv/bin/activate
echo "...DONE"
echo "Extracting PDBs ..."
cd $LOCAL_TASK_DIR
LOCAL_PDB_DIR=$LOCAL_TASK_DIR/pdb
mkdir -p $LOCAL_PDB_DIR
/usr/bin/time $ZIP_EXTRACT -i $ZIP_INDEX_FILE -z $ZIP_DIR -o $LOCAL_PDB_DIR
echo "...DONE"
echo "Running chainsaw ..."
/usr/bin/time $PYTHON_EXE $SHARED_REPO/scripts/get_predictions.py --structure_directory $LOCAL_PDB_DIR -o $RESULTS_FILE \
--model_dir $SHARED_REPO/weight/model_v3 --config_dir $SHARED_REPO/conf/model_v3
echo
echo "Removing local temp dir ..."
rm -rf $LOCAL_TASK_DIR
echo
echo "DATE_FINISHED : "`date`
echo "JOB_COMPLETE"
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