Outputs are created, but a final error is stated / Fatal error:

[SamGG]

Hi,
The tool I am developing runs without any error on command line. I also check the return code ($?). Within Galaxy the process generates all the outputs. But, there is an error that is raised and renders the results with a red background instead of a green one. Strangely enough, I can view the results by clicking on the eye. I have no clue since. The only strange thing is that the stderr starts with “Fatal error:” and continues with all the log messages (more than one hundred lines). Any tip?
Samuel

[jennaj]

Quick clarification questions:

• Are you using Planemo for tool development? https://planemo.readthedocs.io
• And just as a guess, this could be a metadata error. Check if the output datatype is a mismatch for actual data content. What are those datatypes? A single output dataset or multiple?

[SamGG]

Thanks for your tips. Finally I found the error, which was a tar error at some stage of the process.
What was very misleading to me is that the process reached its end whereas the error was in the middle of the whole process and that the “Fatal error:” was written at the beginning of the stderr. Moreover I also get some syntax errors with a green background as result (simple example below). Hopefully it’s solved.

[SamGG]

Thanks for your tips. While I solved an intermittent error, the problem is still present. Finally I discovered that Galaxy adds a ‘Fatal Error:’ line at the beginning of the stderr if there is ‘ERROR’ or ‘error’ somewhere in the stderr of the tool. Try it yourself with the following code in a simple tool.
Hope this help.

<command detect_errors="aggressive">
<![CDATA[
echo << EOF 1>&2
[15:34:56] error: blablabla
[15:34:56] error: bliblibli
EOF
echo Done!
]]>
</command>

[jennaj]

Correct, this is how that command function works, explained here:

https://planemo.readthedocs.io/en/latest/standards/docs/best_practices/tool_xml.html#exit-code-detection

[SamGG]

Thanks. I even miss this in the Galaxy documentation. In fact the word list is larger.