prefetch.3.1.1 err: name not found while resolving query within virtual file system module

[J-Calvelo]

Hello. I ran into this issue while downloading SRA files. Not sure what could be the cause. The SRA were downloaded and as far I can tell are fine. Here is the command and the error message

prefetch SRR29793839 /nfs6/IB/Blouin_Lab/users/javierc/data/PRJNA1133633_Zhang_2024/SRR29793839.sra

##hpcman.jobs={'runid':'676008','runname':'download_ncbi_4','host':'aspen12','wd':'/nfs6/IB/Blouin_Lab/users/javierc/data/PRJNA1133633_Zhang_2024','taskid':'1'}
2025-02-06T05:42:24 prefetch.3.1.1 err: name not found while resolving query within virtual file system module - failed to resolve accession '/nfs6/IB/Blouin_Lab/users/javierc/data/PRJNA1133633_Zhang_2024/SRR29793839.sra' - Cannot resolve accession ( 404 ); ncbi_phid=322CC81C0D9602950000250F54B409AA.1.m_2

[durbrow]

prefetch SRR29793839 /nfs6/IB/Blouin_Lab/users/javierc/data/PRJNA1133633_Zhang_2024/SRR29793839.sra 

This command instructed prefetch to download SRR29793839, which it did, and /nfs6/IB/Blouin_Lab/users/javierc/data/PRJNA1133633_Zhang_2024/SRR29793839.sra, which failed because that is not an accession.

You probably wanted something like:

prefetch SRR29793839 -O /nfs6/IB/Blouin_Lab/users/javierc/data/PRJNA1133633_Zhang_2024 

Then your accession file would be downloaded to /nfs6/IB/Blouin_Lab/users/javierc/data/PRJNA1133633_Zhang_2024/SRR29793839

NB. You should not reference the .sra file directly by name. prefetch it by name and use the directory named for the accession, not the .sra file inside that directory. A run is not always just one file.