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
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
Here is the code of my python script:
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 this error".
About half the time, the results were
- 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:
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
I must say that at the moment, I have
absolutely no idea how to solve this issue.
Many thanks for your help!