Dear Galaxy mailing-list,
We are currently facing a strange issue with our local Galaxy installation (distribution from Jan. 11 2013). I'm going to try to describe the problem as much as I can, and feel free to ask for more details if it can help in solving this issue.
So basically, we have a situation where (about half the time), when a job ends in error, the error message (shown when clicking on the bug icon), doesn't seem to be related to the dataset in error. As this particular problem seem to be present only when datasets ends in error, I created a simple python script which simply does 2 things:
It outputs the hostname to stdout (in order to investigate if the problem is node-dependant) It outputs the following message "This is an error message printed to stderr", to stderr. (This is done in order to get only error datasets and to investigate the before-mentioned issue.)
Here is the code of my python script:
import sys import socket
def main(): print socket.gethostname() sys.stderr.write('This is an error message printed to stderr\n')
if __name__ == '__main__': main()
I ran this tool about 50 times and I looked at the error messages displayed both in the preview section of the dataset (in the history), and the error message displayed when clicking on the bug icon "view or report this error".
About half the time, the results were as expected:
the dataset stdout would read the name of the node where the job was executed the dataset stderr would read: "This is an error message printed to stderr" and the error message displayed when clicking on the bug icon would be:
Dataset generation errors Dataset 54: Test error Tool execution generated the following error message: This is an error message printed to stderr
The tool produced the following additional output: some.server.name
However, the other half of the time, the error message shown in stderr doesn't correspond to the error message displayed when clicking on the bug icon:
the dataset stdout is still reading the name of the node the dataset stderr is still reading "This is an error message printed to stderr" but the error message displayed when clicking on the bug icon would be something like:
Dataset generation errors
Dataset 3: chrM.bed Tool execution did not generate any error messages.
We can clearly see a discrepancy between the error message in stderr and the error message of the bug report. Actually, the bug report is saying that there is not any error and it makes reference to some "Dataset 3: chrM.bed", even when the actual dataset is "Dataset 53: Test error". There is absolutely no .bed file in my history and the dataset 3 actually reads "Dataset 3: Test error". Some of the datasets mentioned in the faulty bug reports seems to be really old datasets (like one year old).
So my question to you is, could this be related to some mix-up between datasets ID? And how can I look this up. I must say that at the moment, I have absolutely no idea how to solve this issue.
Many thanks for your help!
Best regards, Jean-François