Question: Sra to fastq conversion err
2
gravatar for bharathramh
3.3 years ago by
bharathramh30
bharathramh30 wrote:

Im 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 'sra@ncbi.nlm.nih.gov' for assistance.
=============================================================

 

pls resolve it. 

Thanks in advance

software error • 2.4k views
ADD COMMENTlink modified 2.9 years ago by Arnaud Ceol840 • written 3.3 years ago by bharathramh30
2

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)

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Michael Dondrup46k

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 'sra@ncbi.nlm.nih.gov' for assistance.
=============================================================

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

ADD REPLYlink written 3.3 years ago by bharathramh30

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
ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Michael Dondrup46k

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

ADD REPLYlink written 3.3 years ago by Michael Dondrup46k
2
gravatar for piet
3.3 years ago by
piet1.6k
planet earth
piet1.6k wrote:
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
ADD COMMENTlink written 3.3 years ago by piet1.6k
0
gravatar for EagleEye
3.3 years ago by
EagleEye6.2k
Sweden
EagleEye6.2k wrote:

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.

 

ADD COMMENTlink written 3.3 years ago by EagleEye6.2k
0
gravatar for Arnaud Ceol
2.9 years ago by
Arnaud Ceol840
Milan, Italy
Arnaud Ceol840 wrote:

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

vdb-config --restore-defaults
ADD COMMENTlink written 2.9 years ago by Arnaud Ceol840
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