SRA Downloads

What does it do?

SRA Download downloads fastq files from the SRA, saves them on the NAS, uploads them to Azure storage and then assembles them with COWBAT on FoodPort.

How do I use it?

Subject

In the Subject field, put sradownload. Spelling counts, but case sensitivity doesn't.

Description

Required components:

  • In the first line include the run name run_name=[YYMMDD-sra]. This should be the name of the container in Azure storage and the run name in FoodPort
  • The last line(s) should be a list of SRA ID's you would like to download (one per line)

Optional components:

  • email=email_address An email address may be supplied to Foodport so that the user can be notified when the assembly is complete. eg. email=olcbioinforatics@gmail.com
  • basic_assembly This command makes it so COWBAT only performs assembly, but does not run any typing modules
  • preprocess This command makes it so COWBAT only performs quality assessments and read trimming/error correcting. COWBAT will not perform any assembly or typing

Example

For an example of an SRA download, see issue 34216.

How long does it take?

The run should approximately take about 15-20 minutes per SRA ID.

What can go wrong?

Requested SRA IDs are not available. If we can't find some of the SRA IDs that you request, you will get a warning message informing you of it.