How to download multiple SRA files with prefetch in ubuntu?
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.
• 2,004 views
•
link
updated
by
Istvan Albert
•
written
by
Ahmed Ezat El Zowalaty •
•
written
by
Ahmed Ezat El Zowalaty •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Download SRR by parallel and fastq dump with a weird problem
written by diqixiaoyaoer •
-
Problem with fatsq-dump
written by Utpal •
-
Error while downloading the data using SRA Tools
written by usef •
-
Paired-end dataset from SRA database
written by melissachua90 •
-
Efficient way to download SRA dataset
written by melissachua90 •
-
Fastq-dump warning: too many reads at spot id
written by melissachua90 •
-
Bulk download w prefetch but unable to 'zip' (plus more...)
written by j_eag •
-
Downloading multiple studies SRA data through while loop
written by jobrien20 •
-
How to set sleep in GNU parallel in a esearch/efetch script
written by MAPK
-
Bulk download of entire BioProject SRA
written by Anand Rao
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-dumpIn 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.srasuffix. See also Fast download of FASTQ files from the European Nucleotide Archive (ENA) or get direct download links via sra-explorer.infoDon't forget about your network. If you don't have enough bandwidth you may end up killing all downloads.