Get Data > ENA SRA - slow or failed downloads try NCBI instead

Question: Get Data > ENA SRA - slow or failed downloads try NCBI instead

5 months ago by

European Union

h.stotz • 20 wrote:

Dear Jen,

This is becoming quite frustrating. When I use your tool Get Data > ENA SRA it just connects me to the following website:

https://www.ebi.ac.uk/ena/data/search?GALAXY_URL=https%3A//usegalaxy.org/tool_runner%3Ftool_id%3Debi_sra_main

I then go to: https://www.ebi.ac.uk/ena/data/view/SRR3134040 and click on FASTQ files (Galaxy). It opens the link about:blank and nothing happens. I am not sure what to do anymore.

Best wishes,

Henrik

get-data ncbi galaxy ena-sra fastq • 221 views

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modified 5 months ago by Jennifer Hillman Jackson ♦ 25k • written 5 months ago by h.stotz • 20

5 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Their server is very busy right now and using the "(Galaxy)" links from the site directly also seem impacted. I tried to load the data that way and it eventually timed out (no dataset was sent back to my Galaxy session). This is likely a problem on their side due to the server load.

Try using the Get Data tool instead. When the external site opens up, search by the accession, navigate to the data, then use the "Galaxy" link to send over the fastq data. After that, you'll be redirected back to Galaxy automatically and the dataset will load into the same active history you started in.

If the ENA server is load is high, the download will fail with a warning about the ENA site being busy, which confirms the problem. They host a lot of data and at times can be very busy. The only solution is to try again.

Or, you can try the tool NCBI SRA Tools > Download and Extract Reads in FASTA/Q format from NCBI SRA if your accession is there. This data source tends to be less busy. Be aware that data loaded from this source sometimes need to have the format standardized, this is how: FAQ https://galaxyproject.org/support/ > Reformatting fastq data loaded with NCBI SRA https://galaxyproject.org/support/ncbi-sra-fastq/

One of those should work, even if it means waiting until the ENA site is less busy. Thanks! Jen, Galaxy team

ADD COMMENT • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k

I was running a test with this accession and the NCBI tools and it has already started loading. So try using that data source instead as well. ENA is a good source, but busy.

ADD REPLY • link modified 5 months ago • written 5 months ago by Jennifer Hillman Jackson ♦ 25k

The download from NCBI completed and is intact with proper metadata and formatting, ready to use. This should work for you too.

ADD REPLY • link written 5 months ago by Jennifer Hillman Jackson ♦ 25k

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