Downloading files from dbgap

Ask Kushal he learned the lesson the hard way. The downloaded data have. We need sra-toolkit to decode the data next. If use Anaconda on midway2, then it does not allow user to install sra-toolkit. So we need to install the conda by ourthelves:. In order to decrypt, a dbGaP repository key is also required.

Then change the root to the data folder you store the data. See below the change I made to point to that directory. Receive an email about a new dataset available for download. Run the command in the directory you want the data to go, or edit the. Wondering where you should put the data? Read all of the section on decrypting, because the data needs to be inside a certain directory to be decrypted.

The project key necessary for decryption can be found on the My Projects tab of the dbGaP data portal. Hello, I am having this exact same error as well. I have successfully run prefetch with the test SRA file. I'm using the latest docker container version 2. Questions concerning errors when trying to resolve an accession should be sent to sra ncbi. These errors are from servers at NCBI, they don't originate in the toolkit, and there's nothing the toolkit developers can do about it.

Note, this doesn't mean the servers at NCBI are acting wrong, they might be, but it is more likely something else, like the data was withdrawn by the submitter.

For problems concerning access to the data, please contact the SRA data curators using the email address above. Skip to content. Star New issue. Jump to bottom.