[Iplant-api-dev] newbler failure

[Rion Dooley]

What’s your app id? Maybe I can see something going on.

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Rion




On Aug 13, 2014, at 5:55 PM, Barthelson, Roger A - (rogerab) <rogerab at email.arizona.edu<mailto:rogerab at email.arizona.edu>> wrote:

I don’t have any irods commands in my wrapper script, but I’m getting the irods error anyway. And oddly enough, I am getting the input file, FFGLB5S04.sff, too.

Roger
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Roger Barthelson Ph.D.
Scientific Analyst
iPlant Collaborative
BIO5 Institute, University of Arizona
Phone: 520-977-5249
Email: rogerab at email.arizona.edu<mailto:rogerab at email.arizona.edu>
Web: www.iplantcollaborative.org/<http://www.iplantcollaborative.org/>


On August 13, 2014 at 3:38:41 PM, Rion Dooley (dooley at tacc.utexas.edu<mailto:dooley at tacc.utexas.edu>) wrote:

Agave stages all your date to the execution system for you before the job starts running. You don’t need to pull it yourself. Once your job starts, you can find the file(s) or folder(s) you specified in your inputs present in your job work directory. In this case, you will have a file named FFGLB5S04.sff waiting for you at run time.

--
Rion




On Aug 13, 2014, at 4:46 PM, Barthelson, Roger A - (rogerab) <rogerab at email.arizona.edu<mailto:rogerab at email.arizona.edu>> wrote:

I was able to submit a job, have it run and then archive the results successfully now. I used Newbler as my app. The only problem is that the actual job failed. In the .err file there was this:
ERROR: resolveRodsTarget: srcPath /iplant/home/rogerab/FFGLB5S04.sff does not exist
ERROR: getUtil: resolveRodsTarget status = -317000 USER_INPUT_PATH_ERR
terminate called after throwing an instance of 'std::out_of_range’

For some reason, it was looking at the wrong path for the input file. The file path was entered as this in the json file for the job: /rogerab/data/sequencing1/FFGLB5S04.sff.

Roger

--
Roger Barthelson Ph.D.
Scientific Analyst
iPlant Collaborative
BIO5 Institute, University of Arizona
Phone: 520-977-5249
Email: rogerab at email.arizona.edu<mailto:rogerab at email.arizona.edu>
Web: www.iplantcollaborative.org/<http://www.iplantcollaborative.org/>
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