GPFS filesystems will see significant slowdowns in their jobs. Because of this, users with data located on NOTE: The SRA Toolkit executables use random access to read input files. On a Biowulf interactive session, you should allocate local disk and use that instead of /scratch as in the example below. scratch is not accessible from the Biowulf compute nodes.
#Sra toolkit download#
# Note: don't download to /data/$USER, use a subdirectory like /data/$USER/sra fasterq-dump -p -t /scratch/$USER -O /data/$USER/sra SRR2048331 data/$USER/sra which has no other mkdir module load sratoolkit Instead, you must download the data to a new subdirectory, e.g. Sratoolkit versions < 3.0.0: Do not download to the top level of /data/$USER or /home/$USER. To download on Biowulf, don't run on the Biowulf login node use a batch job or interactive job instead. That will get deleted after the download is complete.įor example, on Helix, the interactive data transfer system, you can download as in the example below. During the download, a temporary directory will be created in the location specified by the -t flag (in the example below, in /scratch/$USER) (Note: the old fastq-dump is being deprecated). You can download SRA fastq files using the fasterq-dump tool, which will download the fastq file into your current working directory by default. If you attempt to download non-ETL SRA data from AWS or GCP without the account information, you will see an error message along these lines:īucket is requester pays bucket but no user project provided. The user needs to establish account information, register it with the toolkit, and authorize the toolkit to pass this information to AWS or GCP to pay for egress charges. If requesting "original submission" files in bam or cram or some other format, they can ONLY be obtained from AWS or GCP and will require that the user provide a cloud-billing account to pay for egress charges. prefetch is the only SRAtoolkit tool that provides access to the original bams. Most sratoolkit tools such as fasterq-dump will pull ETL data from NCBI.
In the case of ETL data, Sratoolkit tools on Biowulf will always pull from NCBI, because it is obviously nearer and there are no fees. Users who want access to the original bams can only get them from AWS or GCP today. NCBI maintains only ETL data online, while AWS and GCP have both ETL and original submission format. Two versions of the data exist: the original (raw) submission, and a normalized (extract, transform, load ) version. Amazon Web Services (= 'Amazon cloud' = AWS).SRA Data currently reside in 3 NIH repositories:
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