Sra to fastq conversion err

Question

[bharathramh]

I'm having a err report of in Sra input of my ubuntu 14.04 64 bit architecture.

2016-01-02T08:22:11 fastq-dump.2.5.7 err: name not found while resolving tree within virtual file system module - failed ERR445520.sra

=============================================================
An error occurred during processing.
A report was generated into the file '/home/uday/ncbi_error_report.xml'.
If the problem persists, you may consider sending the file
to '[e-mail]' for assistance.
=============================================================

Please resolve it.

Thanks in advance

[Michael]

Please be considerate, were are not here to resolve your problems in the absence of all information at your disposal. What was your command line? Where is the error report? Did you use the primary support route that is provided in the error message? Did you search for the problem? (You did not)

[bharathramh]

I have given the command as

fastq-dump --split-3 ERR445520.sra

and it showing the error

2016-01-02T08:46:07 fastq-dump.2.5.7 err: name not found while resolving tree within virtual file system module - failed ERR445520.sra

=============================================================
An error occurred during processing.
A report was generated into the file '/home/uday/ncbi_error_report.xml'.
If the problem persists, you may consider sending the file
to '[e-mail]' for assistance.
=============================================================

I'm using ubuntu 14.04 LTS 64 bit. I'm running the command from the folder where the fastq-dump and my sra file is located. but its showing the error msg

[Michael]

Most problem reports with sra tools, and there are quite a lot here, seem to come from cryptic error messages, I give you that. please try

fastq-dump --split-3 `pwd`/ERR445520.sra

[Michael]

https://github.com/ncbi/sra-tools/wiki/FAQ#faq2

Answer 1

[piet]

fastq-dump --split-3 ERR445520.sra

The above command will only work if there exists a SRA file with exactly this name in your current working directory. If you want to download the SRA data from NCBI, you have to supply just the accession without any filename extension:

fastq-dump --split-3 ERR445520

Answer 2

[EagleEye]

Double check the path of the input SRA file. If the path looks fine, then contact NCBI-SRA people (the error looks like there is no problem in path).

Other less common reason:

Sometime you need to give the whole path to the file while using linux with virtual box (rather than regular partition). This happens for some programs but these tools should be able to handle it.

Answer 3

[Arnaud Ceol]

The solution provided here A: sra-toolkit not working worked for me also in this case:

vdb-config --restore-defaults