Question: How to download multiple SRA files with prefetch in ubuntu?
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gravatar for elzow003
10 days ago by
elzow0030
elzow0030 wrote:

I created a download list

grep -E 'SRR|ERR' XDR_169_ids.txt > downloads.txt

## Find SRAs from SRS:
grep 'SRS' XDR_169_ids.txt | parallel "esearch -db sra -query {} | efetch --format runinfo | cut -d ',' -f 1 | grep SRR" >> downloads.txt

## Now make sure there are no duplicates, then download using GNU parallel to have 4 (or as many your disk can handle) streams in parallel:
sort -u downloads.txt | parallel -j 4 "prefetch {}"

Files were not downloaded.

rna-seq • 83 views
ADD COMMENTlink modified 10 days ago by Istvan Albert ♦♦ 85k • written 10 days ago by elzow0030

prefetch does not unpack the files, just prefetches them (places them in a storage system for later commands that need it)

if you want to see files you need to use fastq-dump

ADD REPLYlink modified 10 days ago • written 10 days ago by Istvan Albert ♦♦ 85k

In which folder did you check? It does not load it to the current directory unless you tell it to. Otherwise it goes to the one that is specified in vdb-config -i. There should be files with .sra suffix. See also Fast download of FASTQ files from the European Nucleotide Archive (ENA) or get direct download links via sra-explorer.info

ADD REPLYlink modified 10 days ago • written 10 days ago by ATpoint42k

or as many your disk can handle

Don't forget about your network. If you don't have enough bandwidth you may end up killing all downloads.

ADD REPLYlink modified 10 days ago • written 10 days ago by genomax92k
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