Transdecoder - C.bairdi De Novo Transcriptome from 20191218 on Mox

Ran Trinity to de novo assemble the C.bairdi RNAseq data we had on 20191218 and now will begin annotating the transcriptome using TransDecoder on Mox.

SBATCH script (GitHub):

20191220_cbai_transdecoder.sh

#!/bin/bash
## Job Name
#SBATCH --job-name=transdecoder_cbai
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=25-00:00:00
## 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/20191220_cbai_transdecoder


# Exit script if a command fails
set -e

# Load Python Mox module for Python module availability

module load intel-python3_2017

# 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

# Set workind directory as current directory
wd="$(pwd)"

# Capture date as YYYYMMDD
timestamp=$(date +%Y%m%d)

# Set input file locations and species designation
trinity_fasta="/gscratch/srlab/sam/data/C_bairdi/transcriptomes/20191218.C_bairdi.Trinity.fasta"
trinity_gene_map="/gscratch/srlab/sam/data/C_bairdi/transcriptomes/20191218.C_bairdi.Trinity.fasta.gene_trans_map"
species="cbai"

# Capture trinity file name
trinity_fasta_name=${trinity_fasta##*/}



# Paths to input/output files
blastp_out_dir="${wd}/blastp_out"
transdecoder_out_dir="${wd}/${trinity_fasta_name}.transdecoder_dir"
pfam_out_dir="${wd}/pfam_out"
blastp_out="${blastp_out_dir}/${timestamp}.${species}.blastp.outfmt6"
pfam_out="${pfam_out_dir}/${timestamp}.${species}.pfam.domtblout"
lORFs_pep="${transdecoder_out_dir}/longest_orfs.pep"
pfam_db="/gscratch/srlab/programs/Trinotate-v3.1.1/admin/Pfam-A.hmm"
sp_db="/gscratch/srlab/programs/Trinotate-v3.1.1/admin/uniprot_sprot.pep"



# Paths to programs
blast_dir="/gscratch/srlab/programs/ncbi-blast-2.8.1+/bin"
blastp="${blast_dir}/blastp"
hmmer_dir="/gscratch/srlab/programs/hmmer-3.2.1/src"
hmmscan="${hmmer_dir}/hmmscan"
transdecoder_dir="/gscratch/srlab/programs/TransDecoder-v5.5.0"
transdecoder_lORFs="${transdecoder_dir}/TransDecoder.LongOrfs"
transdecoder_predict="${transdecoder_dir}/TransDecoder.Predict"

# Make output directories
mkdir "${blastp_out_dir}"
mkdir "${pfam_out_dir}"

# Extract long open reading frames
"${transdecoder_lORFs}" \
--gene_trans_map "${trinity_gene_map}" \
-t "${trinity_fasta}"

# Run blastp on long ORFs
"${blastp}" \
-query "${lORFs_pep}" \
-db "${sp_db}" \
-max_target_seqs 1 \
-outfmt 6 \
-evalue 1e-5 \
-num_threads 28 \
> "${blastp_out}"

# Run pfam search
"${hmmscan}" \
--cpu 28 \
--domtblout "${pfam_out}" \
"${pfam_db}" \
"${lORFs_pep}"

# Run Transdecoder with blastp and Pfam results
"${transdecoder_predict}" \
-t "${trinity_fasta}" \
--retain_pfam_hits "${pfam_out}" \
--retain_blastp_hits "${blastp_out}"