prefetch in linux
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8 weeks ago
reza • 0

RNA coding data non SRR • 423 views
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Command line options need spaces at the right places. Reading command line documentation can be challenging for beginners, but it's pretty easy to start learning.

The command you're looking for is:

prefetch --force https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos3/sra-pdb-run-20/SRR10727148/SRR10727148.1


I typed the above URL by eyeballing your screenshot, so it might not be accurate.

When reading docuentation, remember that [..] usually means optional arguments and <...> refers to required parameters.

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thanks a lots Dear Ram

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Seems like you've been hitting copy as HTML rather than copy.

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The existence of <..> does not mean HTML.

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8 weeks ago
ATpoint 52k

It is:

prefetch -O ~/downloads SRR10727148


nothing more. Use -O to specify the output directory. Don't provide http or ftp paths, especially not in > and without any whitespaces, the download links are automatically resolved internally, you only have to give the accession number. Better would be to just use sra-explorer.info to get fastq download links directly to load via curl or wget though.

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thank u Dear ATpoint

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but i didn't get any result

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I can't help with error messages like that as I cannot see your screen. Did you run precisely the above command, if so any status logs, did the command finish? Please do not use the answer field, use ADD REPLY to keep things organized.

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thank u.i sent screen shot

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I do not see any.

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Yeah, the typical cryptic gibberish that this more than unreliable tool produces. Just go to sra-explorer.info, enter the accession and get a download link for the fastq file, done in no time ;-)

Will return something like (I added the wget):

wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR107/048/SRR10727148/SRR10727148_1.fastq.gz
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR107/048/SRR10727148/SRR10727148_2.fastq.gz