Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Error in Extract Reads
1
gravatar for blake.wilde
2.4 years ago by
blake.wilde • 10
blake.wilde • 10 wrote:

Get this error when trying to execute the program "Extract Reads" in Galaxy.

For the input, I used an SRR ascension number (I tried several from different experiments).

Fatal error: Exit code 127 (Could not locate fastq-dump binary) /galaxy-repl/main/jobdir/013/226/13226353/tool_script.sh: line 9: vdb-config: command not found /galaxy-repl/main/jobdir/013/226/13226353/tool_script.sh: line 9: prefetch: command not found

Any ideas why?

Thanks for any input.
extract reads galaxy • 1.0k views
ADD COMMENT • link •
modified 2.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.4 years ago by blake.wilde • 10

Is this at http://usegalaxy.org? Or someplace else?

ADD REPLY • link written 2.4 years ago by Jennifer Hillman Jackson ♦ 25k

It is at http://usegalaxy.org

ADD REPLY • link written 2.4 years ago by blake.wilde • 10

Thank you, testing this. Feedback soon. - Jen, Galaxy team

ADD REPLY • link written 2.4 years ago by Jennifer Hillman Jackson ♦ 25k

I am not able to reproduce the problem. Would you please share one or two of the problematic SRR accessions? I will test with those and see if this error can be triggered.

ADD REPLY • link written 2.4 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks. Yes, one I used was SRR3020343.

ADD REPLY • link written 2.4 years ago by blake.wilde • 10
0
gravatar for Jennifer Hillman Jackson
2.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tools are problematic today when extracting data from NCBI. Track the fix here: https://github.com/galaxyproject/galaxy/issues/2533

Good news is that the data is at EBI SRA. In the far left panel, in the group Get Data, is a tool that can be used to load the data into Galaxy.

How to: https://wiki.galaxyproject.org/Support#Get_Data:__EBI-SRA

Hope this helps! Jen, Galaxy team
ADD COMMENT • link written 2.4 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 175 users visited in the last hour