Gunzip - BGI HiSeq Geoduck Genome Sequencing Data

In preparation to run SpareAssembler, I needed to gunzip the BGI gzipped FASTQ files from 20180327.

Ran the following slurm script on our Mox node:

<code>
#!/bin/bash
## Job Name
#SBATCH --job-name=20180405_geoduck_bgi_gunzip
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes (We only get 1, so this is fixed)
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=30-00:00:00
## Memory per node
#SBATCH --mem=500G
##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/scrubbed/samwhite/bgi_geoduck

for i in /gscratch/scrubbed/samwhite/bgi_geoduck/*.gz; do
    filename="${i##*/}"
    no_ext="${filename%%.*}"
    gunzip < "$i" > "$no_ext".fastq
done
</code>

Results:

Completed in ~45mins. Will proceed with massive geoduck genome assembly!