After creating a de novo assembly of C.bairdi transcriptome v1.6 on 20200518, performing BLASTx annotation on 202000519, and TransDecoder for ORF identification on 20200519, I continued the annotation process by running Trinotate.

Trinotate will perform functional annotation of the transcriptome assembly, including GO terms and an annotation feature map that can be used in subsequent Trinity-based differential gene expression analysis so that functional annotations are carried downstream through that process.

SBATCH script (GitHub):

20200520_cbai_trinotate_transcriptome-v1.6.sh

#!/bin/bash
## Job Name
#SBATCH --job-name=trinotate_cbai_v1.6
## Allocation Definition
#SBATCH --account=coenv
#SBATCH --partition=coenv
## 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/20200520_cbai_trinotate_transcriptome-v1.6

# Exit script if any 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


wd="$(pwd)"
timestamp=$(date +%Y%m%d)


## Paths to input/output files

## New folders for working directory
rnammer_out_dir="${wd}/RNAmmer_out"
signalp_out_dir="${wd}/signalp_out"
tmhmm_out_dir="${wd}/tmhmm_out"

# Input files
## BLASTx
blastx_out="/gscratch/scrubbed/samwhite/outputs/20200519_cbai_diamond_blastx_transcriptome_v1.6/cbai_transcriptome_v1.6.blastx.outfmt6"

## TransDecoder
blastp_out="/gscratch/scrubbed/samwhite/outputs/20200519_cbai_transdecoder_transcriptome-v1.6/blastp_out/20200519.cbai.blastp.outfmt6"
pfam_out="/gscratch/scrubbed/samwhite/outputs/20200519_cbai_transdecoder_transcriptome-v1.6/pfam_out/20200519.cbai.pfam.domtblout"
lORFs_pep="/gscratch/scrubbed/samwhite/outputs/20200519_cbai_transdecoder_transcriptome-v1.6/cbai_transcriptome_v1.6.fasta.transdecoder_dir/longest_orfs.pep"

## Transcriptomics
trinity_fasta="/gscratch/srlab/sam/data/C_bairdi/transcriptomes/cbai_transcriptome_v1.6.fasta"
trinity_gene_map="/gscratch/srlab/sam/data/C_bairdi/transcriptomes/cbai_transcriptome_v1.6.fasta.gene_trans_map"

rnammer_prefix=${trinity_fasta##*/}
prefix="${timestamp}.${rnammer_prefix}.trinotate"

# Output files
rnammer_out="${rnammer_out_dir}/${rnammer_prefix}.rnammer.gff"
signalp_out="${signalp_out_dir}/${prefix}.signalp.out"
tmhmm_out="${tmhmm_out_dir}/${prefix}.tmhmm.out"
trinotate_report="${wd}/${prefix}_annotation_report.txt"

# Paths to programs
rnammer_dir="/gscratch/srlab/programs/RNAMMER-1.2"
rnammer="${rnammer_dir}/rnammer"
signalp_dir="/gscratch/srlab/programs/signalp-4.1"
signalp="${signalp_dir}/signalp"
tmhmm_dir="/gscratch/srlab/programs/tmhmm-2.0c/bin"
tmhmm="${tmhmm_dir}/tmhmm"
trinotate_dir="/gscratch/srlab/programs/Trinotate-v3.1.1"
trinotate="${trinotate_dir}/Trinotate"
trinotate_rnammer="${trinotate_dir}/util/rnammer_support/RnammerTranscriptome.pl"
trinotate_GO="${trinotate_dir}/util/extract_GO_assignments_from_Trinotate_xls.pl"
trinotate_features="${trinotate_dir}/util/Trinotate_get_feature_name_encoding_attributes.pl"
trinotate_sqlite_db="Trinotate.sqlite"

# Generate FastA checksum, for reference if needed.
md5sum ${trinity_fasta} > fasta.checksum.md5

# Make output directories
mkdir "${rnammer_out_dir}" "${signalp_out_dir}" "${tmhmm_out_dir}"

# Copy sqlite database template

cp ${trinotate_dir}/admin/Trinotate.sqlite .

# Run signalp
${signalp} \
-f short \
-n "${signalp_out}" \
${lORFs_pep}

# Run tmHMM
${tmhmm} \
--short \
< ${lORFs_pep} \
> "${tmhmm_out}"

# Run RNAmmer
cd "${rnammer_out_dir}" || exit
${trinotate_rnammer} \
--transcriptome ${trinity_fasta} \
--path_to_rnammer ${rnammer}
cd "${wd}" || exit

# Run Trinotate
## Load transcripts and coding regions into database
${trinotate} \
${trinotate_sqlite_db} \
init \
--gene_trans_map "${trinity_gene_map}" \
--transcript_fasta "${trinity_fasta}" \
--transdecoder_pep "${lORFs_pep}"

## Load BLAST homologies
"${trinotate}" \
"${trinotate_sqlite_db}" \
LOAD_swissprot_blastp \
"${blastp_out}"

"${trinotate}" \
"${trinotate_sqlite_db}" \
LOAD_swissprot_blastx \
"${blastx_out}"

## Load Pfam
"${trinotate}" \
"${trinotate_sqlite_db}" \
LOAD_pfam \
"${pfam_out}"

## Load transmembrane domains
"${trinotate}" \
"${trinotate_sqlite_db}" \
LOAD_tmhmm \
"${tmhmm_out}"

## Load signal peptides
"${trinotate}" \
"${trinotate_sqlite_db}" \
LOAD_signalp \
"${signalp_out}"

## Load RNAmmer
"${trinotate}" \
"${trinotate_sqlite_db}" \
LOAD_rnammer \
"${rnammer_out}"

## Creat annotation report
"${trinotate}" \
"${trinotate_sqlite_db}" \
report \
> "${trinotate_report}"

# Extract GO terms from annotation report
"${trinotate_GO}" \
--Trinotate_xls "${trinotate_report}" \
-G \
--include_ancestral_terms \
> "${prefix}".go_annotations.txt

# Make transcript features annotation map
"${trinotate_features}" \
"${trinotate_report}" \
> "${prefix}".annotation_feature_map.txt

RESULTS

Pretty quick, just under 45 mins:

Output folder:

20200520_cbai_trinotate_transcriptome-v1.6/

Annotation feature map. This can be used to update Trinity-based gene expression matrices like so:

${TRINITY_HOME}/Analysis/DifferentialExpression/rename_matrix_feature_identifiers.pl Trinity_trans.counts.matrix annot_feature_map.txt > Trinity_trans.counts.wAnnot.matrix
20200520.cbai_transcriptome_v1.6.fasta.trinotate.annotation_feature_map.txt

Annotation report (CSV)

20200520.cbai_transcriptome_v1.6.fasta.trinotate_annotation_report.txt

Gene ontology (GO) annotations (TXT)

20200520.cbai_transcriptome_v1.6.fasta.trinotate.go_annotations.txt

SQlite database:

Trinotate.sqlite