Question: sra toolkit prefetch: path not found while resolving tree within virtual file system module
1
gravatar for gilbo
12 months ago by
gilbo20
gilbo20 wrote:

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?

rna-seq sra toolkit prefetch • 1.2k views
ADD COMMENTlink modified 8 months ago by Mike Vermeulen0 • written 12 months ago by gilbo20

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.

ADD REPLYlink written 12 months ago by ATpoint26k
0
gravatar for gilbo
11 months ago by
gilbo20
gilbo20 wrote:

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

ADD COMMENTlink written 11 months ago by gilbo20
0
gravatar for Mike Vermeulen
8 months ago by
Mike Vermeulen0 wrote:

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.

ADD COMMENTlink written 8 months ago by Mike Vermeulen0
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