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SparkLeBLAST

Scalable Parallelization of BLAST Sequence Alignment Using Spark

Dependencies

Scala Build Tool

Used to build SparkLeBLAST (https://www.scala-sbt.org/)

Spark

We conducted our experiments using Spark v2.2.0. (https://archive.apache.org/dist/spark/spark-2.2.0/)

NCBI BLAST

SparkLeBLAST works independent of a specific BLAST version. We recently tested it with BLAST v2.13.0: (https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/)

spark-slurm

For usage on an HPC cluster with SLURM workload manager (details below), there are two approaches:

  1. Use the shipped start_spark_slurm.sbatch script
  2. USe spark-slurm (https://github.com/NIH-HPC/spark-slurm) Note: spark-slurm enables more flexible configurations and logging options. It may need some edits to adapt it to your runtime environment. Our adapted version is available at: (https://github.com/karimyoussef91/spark-slurm)

Usage

HPC Cluster With SLURM Workload Manager

  1. Environment variables
    export SPARK_HOME=<path/to/installed/spark/directory> # Where pre-built Spark was downloaded from dependencies abpve 
    export SPARK_SLURM_PATH=</path/to/spark-slurm> # if using spark-slurm 
    export NCBI_BLAST_PATH=</path/to/ncbi_blast/binaries>
    export SLB_WORKDIR=$(pwd) # Path to SparkLeBLAST root directory
  1. Partitioning and formatting a BLAST database:
    ./SparkLeMakeDB -p <num_partitions> -time <job_time_integer_minutes> -i <input_DB_path> -t <output_partitions_base_path>
  1. Running BLAST search:
   ./SparkLeBLASTSearch.sh -p <num_partitions> -time <job_time_integer_minutes> -q <query_file_path> -db <database_partitions_base_path> -d <spark_logs_path>

Custom Spark Cluster

A version of launch scripts without SLURM will be available soon

Data

Small Data Samples for Testing

  1. Query: https://raw.githubusercontent.com/sparkblastproject/v2/master/bacteria/Galaxy25-%5BGeobacter_metallireducens.fasta%5D.fasta

  2. Database: https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/swissprot.gz

COVID-19 Genomic Diversity Analysis

  1. Preprocessed Query: Compressed file could be found in this repo under covdiv_sample

  2. Database (Compressed Raw Size of 144GB): https://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/nt.gz

Publication

Youssef, Karim, and Wu-chun Feng. "SparkLeBLAST: Scalable Parallelization of BLAST Sequence Alignment Using Spark." 2020 20th IEEE/ACM International Symposium on Cluster, Cloud and Internet Computing (CCGRID). IEEE, 2020.

License

Please refer to the included LICENSE file.