SraToFastQ error

[GWang]

Please respond with the following information as applicable:
 Complete description of the problem (ie what you were trying to do and what went wrong):

2018-02-13T21:56:46 fastq-dump.2.3.5 err: error unexpected while resolving tree within virtual file system module - failed to resolve accession 'SRR4454524' - Obsolete software. See https://github.com/ncbi/sra-tools/wiki ( 406 )
2018-02-13T21:56:46 fastq-dump.2.3.5 err: name incorrect while evaluating path within network system module - Scheme is 'https'
2018-02-13T21:56:46 fastq-dump.2.3.5 err: item not found while constructing within virtual database module - the path 'SRR4454524' cannot be opened as database or table

Job ID if run on a publicly available server. 1632718

If not on Public Server, please share your input files, if possible. If you need to do so privately, let us know.
 
   What were your Parameter values?
   Server Platform (Mac/Linux)?

   Any errors or warnings you see in either stderr.txt, stdout.txt or popup dialogues:


Please note that many common errors can be resolved by searching this forum or taking a look at our documentation: 

* Module Documentation - available from the "documentation" link in the upper right hand corner of the module input page or here: http://software.broadinstitute.org/cancer/software/genepattern/modules
* GenePattern FAQ - http://software.broadinstitute.org/cancer/software/genepattern/FAQ
* GenePattern  Videos - http://software.broadinstitute.org/cancer/software/genepattern/video-tutorials
* GenePattern File Formats - http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide#file-formats
* GenePattern User Guide - http://software.broadinstitute.org/cancer/software/genepattern/user-guide#user-guide
* GenePattern Programmer's Guide - http://software.broadinstitute.org/cancer/software/genepattern/programmers-guide
* GenePattern Release Notes - http://software.broadinstitute.org/cancer/software/genepattern/doc/relnotes/current

[Peter Carr]

The error message on the wiki page (https://github.com/ncbi/sra-tools/wiki) makes it clear ...

ATTENTION:
sra-tools has transitioned to all HTTPS access as of October 7, 2016 with release 2.8.0. It is critically important that you update all of your binaries and your configuration files.

This is in response to OMB memorandum M-15-13 issued on June 8, 2015, requiring all Federal HTTP servers to stop using (simple) HTTP and switch to HTTPS.

Please update your software as soon possible to give some time to ensure continued operation.

Proxy users take note - this complicates proxy usage somewhat. We will create a Wiki page dedicated to supported proxy configuration and firewall settings to help users during the conversion.

This is my first time seeing this error. Thanks for bringing it to our attention. I will file a bug report, but I am not sure when we will have a chance to update the software. I am not that familiar with this module. What are you trying to do? And how important is this to your research?

Best regards,
Peter

[Peter Carr]

fyi, I added a new ticket to our ticketing system, GPAT-2362. We will
address this as soon as we can.

Regards,
Peter

[Peter Carr]

As a stopgap, and for testing, I manually copied the files into your uploads directory. You may have to log out and log back in. Look for the "SRR4454524" folder in your "Files > uploads" tab.

I ran these commands with the sra-toolkit v2.8.1

fastq-dump --split-files --aligned -gzip SRR4454524
gunzip SRR4454524_1.fastq.gz
gunzip SRR4454524_2.fastq.gz

In the interim, until we update the module, I suggest that you run the 'fastq-dump' command locally and then upload the fastq files to the GP server.
If you need help ask your friendly neighborhood software specialist or start here:
    https://github.com/ncbi/sra-tools/wiki
    https://github.com/ncbi/sra-tools/wiki/HowTo:-Access-SRA-Data
    https://github.com/ncbi/sra-tools/wiki/FAQ

Regards,

Peter

On 2/13/18 5:47 PM, GWang wrote:

[GWang]

Peter, 

Thank you so much. Will do that. 

Guocan