Incomplete uploading from ENA's EBI SRA -- Solution: try NCBI SRA instead

Hi, I am trying to download RNA-seq data from the “EBI” website using the “Upload Data”. Unfortunately, only a small amount of data is loaded, for instance, 12 Mb from a 2 GB file. I have repeated this job for many several times, but, each time I encountered this problem.

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Hi @karimi65

We’ve had many reports of data download failures from EBI SRA over the prior week or so (and before that, during various time windows when they were reorganizing data). We aren’t clear on what issues ENA may be having right now – perhaps just high volume – although we’ve also seen some technical problems with the links one can capture from their website.

:arrow_right: Try getting the data from the NCBI SRA instead. Entering URLs in the Upload tool is one method plus there are several dedicated tools. Search the tool panel with the keyword “ncbi” to review the choices.

For fastq data, both of these tools are great choices. The first downloads individual dataset(s); the second sorts the dataset(s) into collections. Full usage options are on each tool’s form. Both are equally “fast” – the Galaxy tool name is simply reflective of the underlying name NCBI gave these functions.

Download and Extract Reads in FASTA/Q format from NCBI SRA

Faster Download and Extract Reads in FASTQ format from NCBI SRA

Hope that works out!

thank you so much for your response, I will definitely try :pray:

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