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Prefetch "Redirected!!!" error (acsp) #45

Closed EBosi closed 8 years ago

EBosi commented 8 years ago

Hi, prefetch is failing and I can't understand why. I'm using prefetch with the following command line: prefetch -t ascp -a "~/.aspera/connect/bin/ascp|~/.aspera/connect/etc/asperaweb_id_dsa.openssh" SRR765378

I'm getting this error:

Redirected!!!

2016-11-07T09:14:41 prefetch.2.3.5 err: name incorrect while evaluating path within network system module - Scheme is 'https'
2016-11-07T09:14:41 prefetch.2.3.5 err: path not found while resolving tree within virtual file system module - 'SRR765378' cannot be found.

Rather mysteriously, the same line worked for the same accession one day before. Could you help me with this issue?

klymenko commented 8 years ago

Please download the latest toolkit from https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software

kwrodarmer commented 8 years ago

Please see the README, which states:

IMPORTANT ANNOUNCEMENT

As was announced in OMB memorandum M-15-13 on June 8, 2015, NCBI and all Federal systems will be transitioning to using HTTPS-only protocols before the end of 2016. This change will affect any software that uses NCBI APIs such as the E-utilities or NCBI software toolkits such as sra-tools, ncbi-vdb or ngs.

The NLM and NCBI may implement the switch to HTTPS-only as early as September 30, 2016.

In particular, software products that depend on sra-tools, ncbi-vdb or ngs may not function as expected after September 30 unless they are properly updated from this site or by the software provider.

If you use software that accesses NCBI SRA data in any way, your software will likely be affected by this change. Please check with your software provider for recent udpates or patches, and be sure to acquire these before September 30.

If you develop software that relies on sra-tools, ncbi-vdb or ngs in any way, you will likely need to update your code so that it accesses NCBI using HTTPS.

We have released new tools with version 2.8.0 that are HTTPS compatible and M-15-13 compliant as of October 7, 2016. Please be certain to update all of your binaries and configuration files.

For additional information on using, configuring, and building the toolkit, please visit our wiki or our web site at NCBI

SRA Toolkit Development Team

EBosi commented 8 years ago

Thank you very much for the timely reply, this basically solved my issue. Just two more questions:

On Mon, Nov 7, 2016 at 5:14 PM, kwrodarmer notifications@github.com wrote:

Please see the README, which states: IMPORTANT ANNOUNCEMENT

As was announced in OMB memorandum M-15-13 https://www.whitehouse.gov/sites/default/files/omb/memoranda/2015/m-15-13.pdf on June 8, 2015, NCBI and all Federal systems will be transitioning to using HTTPS-only protocols before the end of 2016. This change will affect any software that uses NCBI APIs such as the E-utilities or NCBI software toolkits such as sra-tools, ncbi-vdb or ngs.

The NLM and NCBI may implement the switch to HTTPS-only as early as September 30, 2016.

In particular, software products that depend on sra-tools, ncbi-vdb or ngs may not function as expected after September 30 unless they are properly updated from this site or by the software provider.

If you use software that accesses NCBI SRA data in any way, your software will likely be affected by this change. Please check with your software provider for recent udpates or patches, and be sure to acquire these before September 30.

If you develop software that relies on sra-tools, ncbi-vdb or ngs in any way, you will likely need to update your code so that it accesses NCBI using HTTPS.

We have released new tools with version 2.8.0 that are HTTPS compatible and M-15-13 compliant as of October 7, 2016. Please be certain to update all of your binaries https://github.com/ncbi/sra-tools/wiki/Downloads and configuration files.

For additional information on using, configuring, and building the toolkit, please visit our wiki https://github.com/ncbi/sra-tools/wiki or our web site at NCBI http://www.ncbi.nlm.nih.gov/Traces/sra/?view=toolkit_doc

SRA Toolkit Development Team

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/ncbi/sra-tools/issues/45#issuecomment-258880440, or mute the thread https://github.com/notifications/unsubscribe-auth/ABQhmQ0jeQJDEpH5THG2zRE09jg0jNoaks5q705ggaJpZM4Kq_x2 .

kwrodarmer commented 8 years ago

Right now, November 2016, you cannot upgrade using apt-get although it is within our future plans.

Running the tool in question with a -V parameter will print its version. Also, whenever it prints information to the log file, the version appears.