Sam’s Notebook: BLASTx – Clupea pallasii (Pacific herring) liver and testes transcriptomes on Mox

Apparently we’ve had some interest in the Pacific herring transcriptomes (liver and testes) we produced many years ago. As such, Steven asked that I do a quick BLASTx to help annotate these two transcriptomes.

Two FastA files were downloaded from FigShare to Mox with the following commands:

Liver transcriptome:

wget https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/88394/HerringHepaticTranscriptome34300contigs.fa

Testes transcriptome:

wget https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/88395/HerringTesticularTranscriptome31545contigs.fa

Used the UniProtKB database that I downloaded on 20181008 as the blast database.

Here are the SBATCH script files used to run these jobs:

Liver job:

Testes job:

Since the two scripts are fairly short in length, I’ll put the full contents below.

Liver job:

  #!/bin/bash ## Job Name #SBATCH --job-name=herring_blast ## Allocation Definition #SBATCH --account=srlab #SBATCH --partition=srlab ## Resources ## Nodes #SBATCH --nodes=2 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=02-0:00:10 ## Memory per node #SBATCH --mem=120 ##turn on e-mail notification #SBATCH --mail-type=ALL #SBATCH --mail-user=samwhite@uw.edu ## Specify the working directory for this job #SBATCH --workdir=/gscratch/srlab/sam/outputs/20181212_blastx_herring_liver # Load Python Mox module for Python module availability module load intel-python3_2017 # Document programs in PATH (primarily for program version ID) date >> system_path.log echo "" >> system_path.log echo "System PATH for $SLURM_JOB_ID" >> system_path.log echo "" >> system_path.log printf "%0.s-" {1..10} >> system_path.log echo ${PATH} | tr : \\n >> system_path.log # Copy SBATCH script to working directory cp /gscratch/srlab/sam/sbatch_scripts/20181212_herring_liver_blastx.sh . # Make blast database available to blast export BLASTDB=/gscratch/srlab/blastdbs/UniProtKB_20181008/ # Set variables ## BLASTx blastx="/gscratch/srlab/programs/ncbi-blast-2.6.0+/bin/blastx" ## UniProt database uniprot="/gscratch/srlab/blastdbs/UniProtKB_20181008/20181008_uniprot_sprot.fasta" liver_fasta="/gscratch/srlab/sam/data/C_pallasii/transcriptomes/HerringHepaticTranscriptome34300contigs.fa" # Run blastp on UniProt database ${blastx} \ -query ${liver_fasta} \ -db ${uniprot} \ -max_target_seqs 1 \ -outfmt 6 \ -num_threads 56 \ > 20181212.herring.liver.blastx.outfmt6 \ 2> 20181212.herring.liver.blastx.err  

Testes job:

  #!/bin/bash ## Job Name #SBATCH --job-name=herring_blast ## Allocation Definition #SBATCH --account=coenv #SBATCH --partition=coenv ## Resources ## Nodes #SBATCH --nodes=2 ## Walltime (days-hours:minutes:seconds format) #SBATCH --time=02-0:00:10 ## Memory per node #SBATCH --mem=120 ##turn on e-mail notification #SBATCH --mail-type=ALL #SBATCH --mail-user=samwhite@uw.edu ## Specify the working directory for this job #SBATCH --workdir=/gscratch/srlab/sam/outputs/20181212_blastx_herring_liver # Load Python Mox module for Python module availability module load intel-python3_2017 # Document programs in PATH (primarily for program version ID) date >> system_path.log echo "" >> system_path.log echo "System PATH for $SLURM_JOB_ID" >> system_path.log echo "" >> system_path.log printf "%0.s-" {1..10} >> system_path.log echo ${PATH} | tr : \\n >> system_path.log # Copy SBATCH script to working directory cp /gscratch/srlab/sam/sbatch_scripts/20181212_herring_testes_blastx.sh . # Make blast database available to blast export BLASTDB=/gscratch/srlab/blastdbs/UniProtKB_20181008/ # Set variables ## BLASTx blastx="/gscratch/srlab/programs/ncbi-blast-2.6.0+/bin/blastx" ## UniProt database uniprot="/gscratch/srlab/blastdbs/UniProtKB_20181008/20181008_uniprot_sprot.fasta" testes_fasta="/gscratch/srlab/sam/data/C_pallasii/transcriptomes/HerringTesticularTranscriptome31545contigs.fa" # Run blastp on UniProt database ${blastx} \ -query ${testes_fasta} \ -db ${uniprot} \ -max_target_seqs 1 \ -outfmt 6 \ -num_threads 56 \ > 20181212.herring.testes.blastx.outfmt6 \ 2> 20181212.herring.testes.blastx.err