I’m trying to run fast-dump from sra-toolkit using the SRA accession numbers, but have tried 8 different file numbers and a number of different runs with nothing working.
Any advice?
I’m trying to run fast-dump from sra-toolkit using the SRA accession numbers, but have tried 8 different file numbers and a number of different runs with nothing working.
Any advice?
Welcome @victorialindsay!
To confirm:
Download and Extract Reads in FASTA/Q format from NCBI SRA (Galaxy Version 2.9.1.3)
Clarify if different, please.
Then share a few more details:
If you want to post some screenshots back to help clarify please do, then we can troubleshoot more. I’m not aware of any problems with this tool/tool-version at the Galaxy Main server – but there could always be something new. But let’s rule out usage/format issues first.
Thanks!
Hi Jennifer,
I loaded one at a time, and two example accession numbers are ERR2731060 and ERR2731061. Yes to both initial questions.
Since emailing you, I have managed to get several other accession numbers to complete (although having difficulties downloading the Fastq files!) but not these two.
Best regards
Victoria
<admin edit: contact card + email removed retain privacy on the public forum>
Try again now if you haven’t already in the last day or so. Maybe the NCBI server was very busy. The data downloaded Ok for me in a test.
Well, it failed in re-test (timed out).
You could try getting the data using the tool Get Data > EBI SRA
instead (different data provider, same data). Search with the SRR accession then use the send to galaxy (fastq) links. There will be two – one for each end of the pair. That worked for me twice in a row, today.