sra.info

The sra.info command reads an accnos file containing sample names. It uses prefetch and fasterq_dump to download and extract the fastq files. It outputs a file for use with the make.contigs command. The prefetch and fasterq_dump tools developed by NCBI, https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software. To follow along with this tutorial, download the accnos file sra.info accnos file.

Default Settings

The accnos parameter is used to list the samples you wish to download. It is required.

mothur > sra.info(accnos=srainfo.accnos)

The screen output should look like this:

>>>>>  Processing sample SRX7796885 (1 of 5)   <<<<<
/******************************************/

Running command: system("/Users/sarahwestcott/desktop/mothur/TARGET_BUILD_DIRTARGET_BUILD_DIR/tools/prefetch" SRX7796885  -o   /Users/sarahwestcott/desktop/release/SRX7796885.sra )
2020-03-05T13:13:04 prefetch.2.10.1: 1) Downloading 'SRR11175880'...
2020-03-05T13:13:04 prefetch.2.10.1:  Downloading via https...
2020-03-05T13:13:05 prefetch.2.10.1:  https download succeed
2020-03-05T13:13:05 prefetch.2.10.1: 1) 'SRR11175880' was downloaded successfully
2020-03-05T13:13:05 prefetch.2.10.1: 'SRX7796885' has 0 unresolved dependencies

/******************************************/
It took 2 seconds to download sample SRX7796885.
/******************************************/

Running command: system("/Users/sarahwestcott/desktop/mothur/TARGET_BUILD_DIRTARGET_BUILD_DIR/tools/fasterq-dump" /Users/sarahwestcott/desktop/release/SRX7796885.sra  -S -3 --threads 16 -o /Users/sarahwestcott/desktop/release/SRX7796885.fastq )
spots read      : 28,526
reads read      : 57,052
reads written   : 57,052

/******************************************/

...

Options

fasterq

The fasterq parameter allows you to specify location of the fasterq_dump executable. By default mothur will look in its location and the location of MOTHUR_TOOLS if specified at compile time or set through the set.dir(tools=locationOfExternalTools) command.

mothur > sra.info(accnos=srainfo.accnos, fasterq=/usr/bin/fasterq-dump)

prefetch

The prefetch parameter allows you to specify location of the prefetch executable. By default mothur will look in its location and the location of MOTHUR_TOOLS if specified at compile time or set through the set.dir(tools=locationOfExternalTools) command.

mothur > sra.info(accnos=srainfo.accnos, prefetch=/usr/bin/prefetch)

maxsize

The maxsize parameter allows you to limit the size of the files downloaded by prefetch. The default is 20 (20GB). To set the max size to 1G, run this command:

mothur > sra.info(accnos=srainfo.accnos, maxsize=1)

gz

The gz parameter allows you to compress the fastq files. The default is false.

mothur > sra.info(accnos=srainfo.accnos, gz=true)

processors

The processors parameter allows you to specify how many processors you would like to use. The default is all available. NOTE: Windows does not support multiple processors.

mothur > sra.info(accnos=srainfo.accnos, processors=12)

Revisions

  • 1.44.0 First Introduced. #27
  • 1.45.3 Fixes bug with sra.info threads option.