Question: Error in Extract Reads
1
gravatar for blake.wilde
9 months ago by
blake.wilde10
blake.wilde10 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 • 372 views
ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson21k • written 9 months ago by blake.wilde10

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

ADD REPLYlink written 9 months ago by Jennifer Hillman Jackson21k

It is at http://usegalaxy.org

ADD REPLYlink written 9 months ago by blake.wilde10

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

ADD REPLYlink written 9 months ago by Jennifer Hillman Jackson21k

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 REPLYlink written 9 months ago by Jennifer Hillman Jackson21k

Thanks. Yes, one I used was SRR3020343.

ADD REPLYlink written 9 months ago by blake.wilde10
0
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson21k 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 COMMENTlink written 9 months ago by Jennifer Hillman Jackson21k
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