sra toolkit

Question

[Esra]

hello I cannot download sra files. I tried prefetch SRR17055838 and gives this error 2021-12-26T13:48:20 prefetch.2.11.2 err: error unexpected while resolving query within virtual file system module - failed to resolve accession 'SRR17055838' - The object is not available from your location. ( 406 ) 2021-12-26T13:48:20 prefetch.2.11.2: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.

fasterq-dump SRR17055838 2021-12-26T13:53:00 fasterq-dump.2.11.3 err: error unexpected while resolving query within virtual file system module - failed to resolve accession 'SRR17055838' - The object is not available from your location. ( 406 ) Query SRR17055838: Error 406 The object is not available from your location. 2021-12-26T13:53:01 fasterq-dump.2.11.3 err: error unexpected while resolving query within virtual file system module - failed to resolve accession 'SRR17055838' - The object is not available from your location. ( 406 ) 2021-12-26T13:53:01 fasterq-dump.2.11.3 err: invalid accession 'SRR17055838' fasterq-dump quit with error code 3

ı cannot find solution, please help thanks

Answer 1

[ATpoint]

One of those many cryptic error messages of a suboptimal tool. Be smart and enter the accession at sra-explorer.info, it will give you a simple download link you can pull via wget directly for the fastq file.

sra-explorer : find SRA and FastQ download URLs in a couple of clicks

[GenoMax]

SRR17055838 dataset is not available via links from sra-explorer either. It is perhaps too new/restricted access. No links show up for it at ENA (via sra-explorer) and the link for SRA file at NCBI comes up as invalid.

Data Access tab in SRA record lists original fastq file links via AWS/Google. Esra: could try your luck with those.

[millerh1]

Had the same issue as OP but this answer worked for me! Really wish they would prioritize maintaining sratoolkit considering how important it has become for many data mining pipelines

[ATpoint]

One should not do them too bad, after all thousands of users use it successfully each day, and the SRA manages petabyte of data, but if it does not work at a given time one easily gets frustrated.