To continue towards getting our Panopea generosa (Pacific geoduck) genome assembly (v1.0) analyzed with BlobToolKit, per this GitHub Issue, I’ve decided to run each aspect of the pipeline manually, as I continue to have issues utilizing the automatic pipeline. As such, I’ve run BLASTn according to the BlobToolKit “Getting Started” guide on Mox.

SBATCH script (GitHub):

20210415_pgen_blastn-nt_Panopea-generosa-v1.0.sh

#!/bin/bash
## Job Name
#SBATCH --job-name=20210415_pgen_blastn-nt_Panopea-generosa-v1.0
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=10-00:00:00
## 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/20210415_pgen_blastn-nt_Panopea-generosa-v1.0


### BLASTn of P.generosa genome assembly Panopea-generosa-v1.0.fa
### against NCBI nt database.
### In preparation for use in BlobTools2


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

# Set number of CPUs to use
threads=40

# Input/output files
fasta="/gscratch/srlab/sam/data/P_generosa/genomes/Panopea-generosa-v1.0.fa"
blast_db="/gscratch/srlab/blastdbs/20210401_ncbi_nt/nt"

# Programs
blastn="/gscratch/srlab/programs/ncbi-blast-2.10.1+/bin/blastn"


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


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

# Exit script if any command fails
set -e


# Run BLASTn with custom format/settings for use in blobtools2
${programs_array[blastn]} \
-db ${blast_db} \
-query ${fasta} \
-outfmt "6 qseqid staxids bitscore std" \
-max_target_seqs 10 \
-max_hsps 1 \
-evalue 1e-25 \
-num_threads ${threads} \
-out Panopea-generosa-v1.0_blobtools2_blast.out


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

# Capture program options
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 [[ "${program}" == "blastx" ]] \
  || [[ "${program}" == "blastn" ]]; 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

# 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

echo "Finished logging system PATH"

RESULTS

Runtime wasn’t too bad; just a bit over 6hrs:

Output folder:

20210415_pgen_blastn-nt_Panopea-generosa-v1.0/
- BLAST output file (see SBATCH script for custom formatting) for improt to BlobToolKit:
  - 20210415_pgen_blastn-nt_Panopea-generosa-v1.0/Panopea-generosa-v1.0_blobtools2_blast.out

After DIAMOND BLASTx and minimap2 alignments are complete, I’ll get this info imported into the BlobToolKit viewer.