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prefetch error: "path invalid while opening directory within file system module - could not build vfs-resolver" #666

Closed afowler56 closed 1 year ago

afowler56 commented 2 years ago

Hello,

I am attempting to download RNA-seq read files from an approved access request through dbGaP using SRA Toolkit. I followed the install instructions for SRA Toolkit found here (https://github.com/ncbi/sra-tools/wiki/02.-Installing-SRA-Toolkit) and the download instructions found here (https://www.ncbi.nlm.nih.gov/books/NBK570248/#Dwnld_DownloadData.Download_Procedure) and here (https://www.ncbi.nlm.nih.gov/sra/docs/sra-dbgap-download/).

After downloading the dbGaP repository key and the cart file from SRA, I used the following code in Command Prompt on my desktop computer, which runs MS Windows 10 (file names have been modified for confidentiality reasons): C:\Users\afowler\Desktop\sratoolkit.3.0.0-win64\bin>prefetch --ngc /Users/afowler/Desktop/ngc_file.ngc /Users/afowler/Desktop/cart_file.krt

And received the following output:

2022-06-28T20:50:41 prefetch.3.0.0 warn: libs/kfs/win/sysdir.c:842:KSysDirMakeSimulatedFSPath: path invalid while opening directory within file system module - could not build vfs-resolver
2022-06-28T20:50:41 prefetch.3.0.0 int: libs/vfs/manager.c:3218:VFSManagerGetResolver: tree NULL while accessing manager within virtual file system module – VFSManagerGetResolver

I would appreciate any advice you may have.

Thank you!

klymenko commented 2 years ago

Email to sra-tools@ncbi.nlm.nih.gov.

afowler56 commented 2 years ago

Already did! They didn't really know how to help me, so I just wanted to cover all my bases by asking here as well. I think it might be a problem with my computer, so I've contacted IT for my organization. If you have any other ideas, I'd really appreciate any advice. Thanks!

klymenko commented 2 years ago

What is case number?

afowler56 commented 2 years ago

case #CAS-915667-Y4G1Q7

cmatKhan commented 1 year ago

Getting the same error -- was there any useful resolution to this?

klymenko commented 1 year ago

@cmatKhan, email to sra-tools@ncbi.nlm.nih.gov.

klymenko commented 1 year ago

Could you try our latest release? Do you still have this problem?

cmatKhan commented 1 year ago

I emailed the helpdesk back in February and somehow this was resolved, I believe on the server end. My submission cmd remained the same, but it started working after emailing.

I think I have the data that I have been asked to gather at this point, but the next time I need to pull data I'll make sure to update