Transcriptome Annotation - Hematodinium Transcriptomes v1.6 v1.7 v2.1 v3.1 with DIAMOND BLASTx on Mox

2020
Miscellaneous
Author

Sam White

Published

August 14, 2020

Needed to annotate the Hematodinium sp. transcriptomes that I’ve assembled using DIAMOND BLASTx. This will also be used for additional downstream annotation (TransDecoder, Trinotate):

All of the above transcriptomes were assembled with different combinations of the crab RNAseq data we generated. Here’s a link to an overview of the various assemblies:

DIAMOND BLASTx was run on Mox.

SBATCH script (GitHub):

#!/bin/bash
## Job Name
#SBATCH --job-name=hemat_diamond_blastx_v1.6_v1.7_v2.1_v3.1
## Allocation Definition
#SBATCH --account=coenv
#SBATCH --partition=coenv
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=0-08:00:00
## 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/20200814_hemat_diamond_blastx_v1.6_v1.7_v2.1_v3.1


## Script for running BLASTx (using DIAMOND) to annotate
## Hematodinium transcriptomes v1.6, v1.7, v2.1 and v3.1 against SwissProt database.
## Output will be in standard BLAST output format 6.

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

# Programs array
declare -A programs_array
programs_array=(
[diamond]="/gscratch/srlab/programs/diamond-0.9.29/diamond"
)

# Establish variables for more readable code
transcriptomes_dir=/gscratch/srlab/sam/data/Hematodinium/transcriptomes

# Array of the various comparisons to evaluate
# Each condition in each comparison should be separated by a "-"
transcriptomes_array=(
"${transcriptomes_dir}"/hemat_transcriptome_v1.6.fasta \
"${transcriptomes_dir}"/hemat_transcriptome_v1.7.fasta \
"${transcriptomes_dir}"/hemat_transcriptome_v2.1.fasta \
"${transcriptomes_dir}"/hemat_transcriptome_v3.1.fasta
)

# DIAMOND UniProt database
dmnd=/gscratch/srlab/blastdbs/uniprot_sprot_20200123/uniprot_sprot.dmnd

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

# Exit script if any command fails
set -e

# Load Python Mox module for Python module availability

module load intel-python3_2017


for fasta in "${!transcriptomes_array[@]}"
do

  # Remove path from transcriptome using parameter substitution
  transcriptome_name="${transcriptomes_array[$fasta]##*/}"

  # Generate checksums for reference
  md5sum "${transcriptomes_array[$fasta]}">> fasta.checksums.md5

  # Run DIAMOND with blastx
  # Output format 6 produces a standard BLAST tab-delimited file
  ${programs_array[diamond]} blastx \
  --db ${dmnd} \
  --query "${transcriptomes_array[$fasta]}" \
  --out "${transcriptome_name}".blastx.outfmt6 \
  --outfmt 6 \
  --evalue 1e-4 \
  --max-target-seqs 1 \
  --block-size 15.0 \
  --index-chunks 4
done


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

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


# Capture program options
for program in "${!programs_array[@]}"
do
    {
  echo "Program options for ${program}: "
    echo ""
    ${programs_array[$program]} --help
    echo ""
    echo ""
    echo "----------------------------------------------"
    echo ""
    echo ""
} &>> program_options.log || true
done

RESULTS

Just under 40 seconds (!!) to annotate the four transcriptomes:

DIAMOND BLASTx cumulative runtime

Output folder:

hemat_transcriptome_v1.6.fasta.blastx.outfmt6
hemat_transcriptome_v1.7.fasta.blastx.outfmt6
hemat_transcriptome_v2.1.fasta.blastx.outfmt6
hemat_transcriptome_v3.1.fasta.blastx.outfmt6