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
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:
sys.stderr.write('This is an error message printed to stderr\n')
if __name__ == '__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
About half the time, the results were as expected:
the dataset stdout would read the name of the node where the job was
the dataset stderr would read: "This is an error message printed to
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:
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
the dataset stdout is still reading the name of the node
the dataset stderr is still reading "This is an error message printed to
but the error message displayed when clicking on the bug icon would be
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
Many thanks for your help!