---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
date: 2018-04-04 21:13:58+00:00
layout: post
slug: gunzip-trimmed-illumina-hiseq-genome-sequencing-data
title: 'Gunzip - Trimmed Illumina Geoduck HiSeq Genome Sequencing Data '
categories:
  - 2018
  - Geoduck Genome Sequencing
tags:
  - geoduck
  - gunzip
  - mox
  - Panopea generosa
---

In preparation to run SpareAssembler, I needed to gunzip the [trimmed gzipped FASTQ files from 20140401](https://robertslab.github.io/sams-notebook/posts/2018/2018-04-01-trimgalorefastqcmultiqc-illumina-hiseq-genome-sequencing-data-continued/).

Ran the following slurm script on our Mox node:


    
    <code>
    #!/bin/bash
    ## Job Name
    #SBATCH --job-name=20180404_geoduck_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/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck
    
    for i in /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/*.gz; do
        filename="${i##*/}"
        no_ext="${filename%%.*}"
        gunzip < "$i" > "$no_ext".fastq
    done
    </code>





##### Results:



This crashed shortly after initiating the run (~30mins later). Received following email notification:



<blockquote>
  SLURM Job_id=155940 Name=20180404_geoduck_gunzip Failed, Run time 00:30:40, NODE_FAIL
</blockquote>



It did not generate a slurm output file, nor any gunzipped files. Will contact UW IT...



##### UPDATE 20140404



Weird, about an hour after this crashed, I received the following email, indicating the job was submitted (I did no resubmit, btw):



<blockquote>
  SLURM Job_id=155940 Name=20180404_geoduck_gunzip Began, Queued time 00:02:29
</blockquote>



Completed about 3hrs later.
