Prefetch doesnt download SRA file in version 2.10.8

[bapoorva]

Hi,

I recently updated my sratoolkit from version 2.8 to 2.10.8. Now my prefetch command doesnt seem to be working.

I tried this prefetch -p SRR8387813 -o ~/SRAfiles/sra. It runs for some 5-10 mins. No progress messages despite the -p argument. No error messages. But then the file doesn't get downloaded either. How do I solve this ?

Thanks,
Apoorva

[bapoorva]

Anyone else having the same issue or any idea on how to fix this ?

[durbrow]

Could you try cd ~/SRAfiles/sra ; prefetch -p SRR8387813 ? Do you get the same result?

[bapoorva]

Yes. I still have the same issue. prefetch works fine when I run it locally. But I want to download the files to a remote server that I'm logged in to using secure shell so that i can process the raw files. This server has sratoolkit installed. fast-dump works on it. Just not prefetch.

[durbrow]

Were you able to run fastq-dump on the remote system without a prefetched copy of the data?

[bapoorva]

yes. For now I've been using prefetch on my local system, uploading all sra files to the remote system and then using fastq-dump on that. It is a very time consuming process.

[durbrow]

What sort of system is the remote? Is it a cloud compute system, like AWS or GCP?

[bapoorva]

Turns out the server doesn't have an outbound network access. My bad. Sorry. Closing issue now

[durbrow]

You might be able to use sshfs to mount a directory from your server as a local directory on your host, and then prefetch into it.