sra toolkit prefetch: path not found while resolving tree within virtual file system module

Question

[gilbo]

Hi all,

Was wondering if anyone can enlighten me as to below. I've been troubleshooting this for several hours but can't figure it out. There seems to be an error where prefetch can't find the accession on ncbi. For example, the following line trying to fetch the example "SRR390728" given in sra docs:

~/sratoolkit.2.9.2-ubuntu64/bin/prefetch SRR390728
2018-11-18T15:43:02 prefetch.2.9.2 err: path not found while resolving tree within virtual file system module - 'SRR390728' cannot be found.

I've configured vdb-config correctly as best as I can tell. I feel that it's probably something simple. Any suggestions?

[ATpoint]

I've configured vdb-config correctly

There is actually nothing you have to set for unrestricted downloads. What did you do? Alternatively, as these data are unrestricted, download them directly as fastq from ENA. You may have a look at my tutorial on that matter if you plan to download larger amounts of data from ENA.

Answer 1

[gilbo]

The long answer is that I had been attempting to download restricted information which is why vdb-config needed configured. Ultimately I found that prefetch wasn't working with even the example request. As it turns out, the IP address I was working with at been blacklisted for reasons not related to this. Once I switched IP addresses I had no issues. If anyone else as this issue, keep that in the differential.

Thanks

Answer 2

[Mike Vermeulen]

I'm getting the same error but only when attempting to download specific SRR files. If I try to download SRR files with DATASTORE_FILETYPE=cram I get the error "cant be found", but if I download files with DATASTORE_FILETYPE=sra they download fine.

I have already set up access keys for GTEx data, and the downloads are fine, with the exception of these cram SRRs.

It downloads sometimes so it couldnt be a blacklisted problem.

[jlergajaso]

Did you solve this? I have the same problem...