How long does it take to create single-end and pair-end data (fastq-dump) from SRAs?

usegalaxy.org support
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Hi!
I am currently running an analysis using the Galaxy platform. I am very new to this platform and still learning. However, I am just wondering how long does it take to download and extract reads in fasta/q format from NCBI SRA. I have 783 SRAs that I want to analyze and up to this moment, I haven’t see any progress on it as you can see in the picture. I have followed the proper importing of SRAs from NCBI up to downloading and extracting of reads; and yet, I see no improvement.

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I hope I can get answer to this.

Thank you!

1 Like
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Welcome @jsscbwng

Those will be large jobs given the number of SRR accessions.

How long it takes to load will depend somewhat on the size of those datasets.

You also might run into problems, during Upload and when working with them downstream, due to the number of datasets.

Allow the job to complete. If it fails we can follow up from there about your options.

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I’m sort of new to galaxy too, but I had downloaded some SRA sequences and in average it took about one minute per sequence (with ascp).

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Thank you!