Hi there,
How to download all SRR files of SRP027383 at once ? What I found on internet guides downloading only one SRR file.
Thanks in advance
This method requires you to have E-utilities and GNU Parallel installed:
esearch -db sra -query SRP027383 | esummary | xtract -pattern DocumentSummary -element Run@acc | parallel -j 1 'fastq-dump -A {}'
Change the number next to the '-j' flag to run N jobs in parallel
What do you want to gain by running it in parallel? This is about downloading 300 SRA files with about 3 gigs each. Bandwidth will be the limiting factor. Also make sure that you have enough free disk space in your HOME or wherever fastq-dump will create its local file cache.
parallel -j 1 would be just a single job at a time, and it certainly looks more elegant than a for loop. Has features such as --progress and --eta. And I think running this with -j 2 would be fine (depending on your architecture) and already double the speed of just sequential downloading.
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Have a look at:
It worked. Thank you !
Dear Wouter.
Downloading process stopped. the following message appears: Error in download.file(i, destfile = file.path(destDir, basename(i)), : write failed If I start to redo downloading, it will again download the existing sra files ! Can you please guide me how to fix it ?
From my links, which command are you using? Is your hard drive full?
The second one, I guessed the memory capacity is the problem so I changed the directory to an external hardware of 1TB. Again it restarts downloading the existing file !
Yes the command simply downloads the entire set without checking what's already available. I don't know what the easiest solution to that is in R. If you would use the answer below here (A: Download SRA data via SRA Toolkit.) you would simply grep those out from the list.