Question: Problems with NCBI SRA file extraction tool
gravatar for efraim.culfa
2.1 years ago by
efraim.culfa0 wrote:


I want to analyse a publicly available data. I first downloaded it from NCBI as an "sra"file and then uploaded it to GALAXY. First, I wanted to see how the data looked like and when i clicked on the eye icon, there appeared alot of "?" icons where the sequence was supposed to be. I still continued and tried quality control which ended up giving "Fatal error: Exit code 1 ()". What could be the problem?

error corrections sra ncbi tool • 683 views
ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson25k • written 2.1 years ago by efraim.culfa0
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This is odd. If you want to send in a bug report, we can review. This tool just went through an update and it may not be quite intact yet.

I'd send you the link to the open ticket, but Github is up/down today (along with many other public servers of all types!).

The workaround is to download the data directly using NCBI tools then uploading to Galaxy via FTP. Or, if the data is at EBI SRA, extract from there using the tool under "Get Data". Note that imports from EBI-SRA have been a bit problematic lately due to connectivity issues with that data provider. If an extract job fails, just re-run it till it works - there isn't another solution.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.1 years ago by Jennifer Hillman Jackson25k
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