ashishfeb13 / alphafold-pdb_mmcif_download-on-hpc

alphafold pdb_mmcif_download on hpc without error

AlphaFold pdb_mmcif_download-on-hpc

Get in Touch

• Email: [e-mail], [e-mail]

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alphafold pdb_mmcif_download on hpc without error

1# Slurm Script for Downloading MMCIF Data

Overview

This script uses Slurm directives to download mmCIF data from rsync mirrors. It fetches files from rsync.rcsb.org and saves them to a specified directory.

Steps:

1. Set Up:

   • Ensure the Slurm environment is available.
   • Modify the script according to the destination directory where files will be downloaded (/path/to-download-pdb_mmcif-data/).

2. Script Execution:

   • Submit the script to Slurm using sbatch script.s (replace script.sh with your actual script filename).

3. Monitoring:

   • Check the logs (Job_%A_%a.out and Job_%A_%a.err) for download progress and errors.
   • Review the log.txt file for download start and finish times.

Notes:

• Update the destination directory (/path/to-download-pdb_mmcif-data/) before execution.
• Check Slurm documentation for any specific configurations required. ########### script ############## #!/bin/bash

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Slurm script to download mmCIF data from mirrors

Script by: Ashish Jaiswal

Contact: [e-mail]

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#SBATCH -o Job_%A_%a.out #SBATCH -e Job_%A_%a.err #SBATCH -n 1 #SBATCH --cpus-per-task=12 #SBATCH --mem=2GB #SBATCH --time=168:00:00 ## time for 7days 168:00:00 #SBATCH --job-name=alphafold #SBATCH --output=alphafold-download #SBATCH --mail-type=END #SBATCH --mail-user=

Log start time in log.txt

echo "-- Started pdb_mmcif files download at $(date)" > log.txt

Downloading mmcif files from rsync mirrors

rsync --bwlimit=1000 --timeout=600 --recursive --links --perms --times --compress --info=progress2 --delete --port=33444 rsync.rcsb.org::ftp_data/structures/divided/mmCIF/ /path/to-download-pdb_mmcif-data/

* ftp.pdbj.org::ftp_data/structures/divided/mmCIF/ (Asia)

Log end time in log.txt

echo "-- Finished pdb_mmcif files download at $(date)" >> log.txt

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rsync options

Running rsync to fetch all mmCIF files (note that the rsync progress estimate might be inaccurate)...

If the download speed is too slow, try changing the mirror to:

* rsync.ebi.ac.uk::pub/databases/pdb/data/structures/divided/mmCIF/ (Europe)

* ftp.pdbj.org::ftp_data/structures/divided/mmCIF/ (Asia)

or see https://www.wwpdb.org/ftp/pdb-ftp-sites for more download options.

All source args must come from the same machine.

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