Question: How to configure Galaxy to fix the error: fastq-dump-paired tool can't fetch SRA file from accession number?
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gravatar for kvas1936
12 months ago by
kvas193620
kvas193620 wrote:

How to configure Galaxy to fix the error: fastq-dump-paired tool can't fetch SRA file from accession number?

ADD COMMENTlink modified 12 months ago by Jennifer Hillman Jackson23k • written 12 months ago by kvas193620
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gravatar for Jennifer Hillman Jackson
12 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

There are some issues with Galaxy Main at http://usegalaxy.org. Please follow here for details and updates: https://biostar.usegalaxy.org/p/20698/

This error may have been due to recent server issues. Once resolved, rerun the job to eliminate that cause. If it fails again, we can help examine job inputs what the root cause is (malformed accession number or a true tool problem). Start with sharing the accession number as directly entered on the tool form (or share a screenshot of the form filled in). We may ask for a bug report to be send in, but the inputs can be examined and server issues fixed first.

Should you be working on a different server, I can let you know that the tool Get Data: EBI SRA is known to fail at times due to connection issues with the data provider (unrelated to Galaxy, and to my knowledge occurs across all deployment types - public server, personal/shared local and/or cloud, custom docker builds - all). Sometimes it takes a few tries to exact certain datasets. The tools that extract data from NCBI can be an alternative - unless these are the tools in use? If so and working at Galaxy Main, the server issues are almost certainly a factor.

Thanks for posting about the problem, Jen, Galaxy team

ADD COMMENTlink modified 12 months ago • written 12 months ago by Jennifer Hillman Jackson23k
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