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I am running the Picard tool CollectSequencingArtifactMetrics in galaxy (locally in my pc).

The output files are saved into disk and not passed to stdout and (I guess) they can't be passed as output from picad to galaxy .

In the xml file I am including:

<outputs>
    <data name='preSummary' format="tabular"  from_work_dir="pref.pre_adapter_summary_metrics"/>
</outputs>



When I click on View details, in "stderr", I see:

[Mon Mar 11 13:43:07 EDT 2019] picard.analysis.artifacts.CollectSequencingArtifactMetrics done. Elapsed time: 0.19 minutes. Runtime.totalMemory()=3323461632

1 - It looks like it worked but shouldn't I see the highlighted information in "stdout" rather than in the "stderr"?
2- If it worked, How can I get my output files? I tracked the working directory printing pwd from the <command> but I guess all files are deleted immediately once the picard process has finished.


Any idea of what am I doing wrong?

What basic knowledge am I missing here?

Thank you!

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  1. Picard, like most tools, prints logs to stderr.
  2. It should be in the Galaxy history. Are you using a version of picard from the toolshed (if so, which one)? You might set cleanup_job to never in the config, which will prevent galaxy from cleaning the working directory. This will enable seeing what the job actually produced.

Most likely there's more in the log file that you're not showing is us and picard itself never ran to completion. In lieu of that information, what I wrote above is usually sufficient to debug things.

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  • $\begingroup$ Picard was running (exit status was 0 when I set to 1 if there was an error) The log was the same as when I run the command in the terminal. I just excluded the prefix "./" in naming the output and it worked (I guess galaxy add a path to the filename with is not "./" ?). Thanks! $\endgroup$
    – aerijman
    Mar 12 '19 at 15:44

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