Sequencing Read Taxonomic Classification - P.verrucosa E5 RNA-seq Using DIAMOND BLASTx and MEGAN daa-meganizer on Mox

2023
E5
Author

Sam White

Published

February 21, 2023

After some discussion with Steven at Science Hour last week regarding the handling of endosymbiont sequences in the E5 P.verrucosa RNA-seq data, Steven thought it would be interesting to run the RNA-seq reads through MEGAN6 just to see what the taxonomic breakdown looks like. We may or may not (probably not) separating reads based on taxonomy. In the meantime, we’ll still proceed with HISAT2 alignments to the respective genomes as a means to separate the endosymbiont reads from the P.verrucosa reads.

The process involves the following:

  1. DIAMOND BLASTx sequencing reads. Generates the appropriate .daa output file for import into MEGAN6.

    • Used a DIAMOND-formatted BLAST database of the NCBI nr database, combined with NCBI taxonomic dump files.

  2. “MEGANize” the DIAMOND BLASTx file using the MEGAN6 tool, daa-maganizer. This prepares the .daa file for import into MEGAN6.

SBATCH Script (GitHub):

#!/bin/bash
## Job Name
#SBATCH --job-name=20230221-pver-diamond-meganizer-E5_RNAseq
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=12-00:00:00
## Memory per node
#SBATCH --mem=120G
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=samwhite@uw.edu
## Specify the working directory for this job
#SBATCH --chdir=/gscratch/scrubbed/samwhite/outputs/20230221-pver-diamond-meganizer-E5_RNAseq

## Perform DIAMOND BLASTx on trimmed P.verrucosa RNA-seq files from 20230215.
## Will be used to view taxonomic breakdown of sequencing reads.

## Expects input FastQ files to be match this pattern: *.fastp-trim.20230215.fq.gz


###################################################################################
# These variables need to be set by user

## Assign Variables

fastq_pattern='*.fastp-trim.20230215.fq.gz'

# Program paths
diamond=/gscratch/srlab/programs/diamond-v2.1.1/diamond
meganizer=/gscratch/srlab/programs/MEGAN-6.22.0/tools/daa-meganizer

# DIAMOND NCBI nr database
dmnd_db=/gscratch/srlab/blastdbs/20230215-ncbi-nr/20230215-ncbi-nr.dmnd

# MEGAN mapping files
megan_mapping_dir=/gscratch/srlab/sam/data/databases/MEGAN
megan_mapdb="${megan_mapping_dir}/megan-map-Feb2022.db"

# FastQ files directory
fastq_dir=/gscratch/srlab/sam/data/P_verrucosa/RNAseq

# CPU threads
threads=40

# MEGAN memory limit
mem_limit=100G

# Programs associative array
declare -A programs_array
programs_array=(
[diamond]="${diamond}" \
[meganizer]="${meganizer}"
)

###################################################################################################

# Exit script if any command fails
set -e

# Load Python Mox module for Python module availability
module load intel-python3_2017


# Loop through FastQ files, log filenames to fastq_list.txt.
# Run DIAMOND on each FastQ, followed by "MEGANization"
# DO NOT QUOTE ${fastq_pattern}
for fastq in "${fastq_dir}"/${fastq_pattern}
do
    # Log input FastQs
    echo ""
    echo "Generating MD5 checksum for ${fastq}..."
    md5sum "${fastq}" | tee --append input_fastqs-checksums.md5
    echo ""

    # Strip leading path and extensions
    no_path=$(echo "${fastq##*/}")
    no_ext=$(echo "${no_path%%.*}")

    # Run DIAMOND with blastx
    # Output format 100 produces a DAA binary file for use with MEGAN
    echo "Running DIAMOND BLASTx on ${fastq}."
    echo ""
    "${programs_array[diamond]}" blastx \
    --db ${dmnd_db} \
    --query "${fastq}" \
    --out "${no_ext}".blastx.meganized.daa \
    --outfmt 100 \
    --top 5 \
    --block-size 15.0 \
    --index-chunks 4 \
    --memory-limit ${mem_limit} \
    --threads ${threads}
    echo "DIAMOND BLASTx on ${fastq} complete: ${no_ext}.blastx.meganized.daa"
    echo ""

    # Meganize DAA files
    # Used for ability to import into MEGAN6
    echo "Now MEGANizing ${no_ext}.blastx.meganized.daa"
    "${programs_array[meganizer]}" \
    --in "${no_ext}".blastx.meganized.daa \
    --threads ${threads} \
    --mapDB ${megan_mapdb}
    echo "MEGANization of ${no_ext}.blastx.meganized.daa completed."
    echo ""

done

# Generate MD5 checksums
for file in *
do
  echo ""
  echo "Generating MD5 checksums for ${file}:"
  md5sum "${file}" | tee --append checksums.md5
  echo ""
done

# Generate checksum for MEGAN database(s)
{
    md5sum "${megan_mapdb}"
    md5sum "${dmnd_db}"
} >> checksums.md5

#######################################################################################################

# Capture program options
if [[ "${#programs_array[@]}" -gt 0 ]]; then
  echo "Logging program options..."
  for program in "${!programs_array[@]}"
  do
    {
    echo "Program options for ${program}: "
    echo ""
    # Handle samtools help menus
    if [[ "${program}" == "samtools_index" ]] \
    || [[ "${program}" == "samtools_sort" ]] \
    || [[ "${program}" == "samtools_view" ]]
    then
      ${programs_array[$program]}

    # Handle DIAMOND BLAST menu
    elif [[ "${program}" == "diamond" ]]; then
      ${programs_array[$program]} help

    # Handle NCBI BLASTx menu
    elif [[ "${program}" == "blastx" ]]; then
      ${programs_array[$program]} -help
    fi
    ${programs_array[$program]} -h
    echo ""
    echo ""
    echo "----------------------------------------------"
    echo ""
    echo ""
  } &>> program_options.log || true

    # If MultiQC is in programs_array, copy the config file to this directory.
    if [[ "${program}" == "multiqc" ]]; then
      cp --preserve ~/.multiqc_config.yaml multiqc_config.yaml
    fi
  done
  echo "Finished logging programs options."
  echo ""
fi


# Document programs in PATH (primarily for program version ID)
echo "Logging system $PATH..."
{
date
echo ""
echo "System PATH for $SLURM_JOB_ID"
echo ""
printf "%0.s-" {1..10}
echo "${PATH}" | tr : \\n
} >> system_path.log
echo "Finished logging system $PATH."

RESULTS

This took a fair amount of time to run and I had to restart a couple of times to continue where it left off. Thus, I don’t have a default “runtime” screencap like I usually do. But, it took ~ 3 weeks. Additionally, the output files are all very large (~100GB each!).

Output folder:

The resulting MEGANized DIAMOND BLASTx DAA files can now be imported into MEGAN6 to visualize/quantify read classification across taxonomic groups. Additionally, MEGAN6 can also be used to separate reads based on taxonomy, if desired.

List of all MEGANized DAA output files: