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Hi everyone. I just updated from Sarek 3.5.1 to 3....
# sarek
m
Hi everyone. I just updated from Sarek 3.5.1 to 3.10.0 I'm noticing a lot of Java stack info in the logs that wasn't there before. It looks like exception stack calls, but nothing is failing, it just has tons of this sort of thing:
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at org.pf4j.DefaultExtensionFinder.find(DefaultExtensionFinder.java:45)
	at org.pf4j.AbstractPluginManager.getExtensions(AbstractPluginManager.java:635)
	at nextflow.plugin.PluginsFacade.getExtensions(PluginsFacade.groovy:329)
	at nextflow.plugin.Plugins.getExtensions(Plugins.groovy:61)
	at nextflow.config.ConfigValidator.loadPluginScopes(ConfigValidator.groovy:75)
	at nextflow.config.ConfigValidator.<init>(ConfigValidator.groovy:70)
	at nextflow.cli.CmdRun.run(CmdRun.groovy:405)
	at nextflow.cli.Launcher.run(Launcher.groovy:526)
	at nextflow.cli.Launcher.main(Launcher.groovy:686)
	at org.pf4j.PluginClassLoader.loadClass(PluginClassLoader.java:169)
	at org.pf4j.AbstractExtensionFinder.find(AbstractExtensionFinder.java:140)
	at org.pf4j.AbstractExtensionFinder.find(AbstractExtensionFinder.java:61)
	at org.pf4j.DefaultExtensionFinder.find(DefaultExtensionFinder.java:45)
	at org.pf4j.AbstractPluginManager.getExtensions(AbstractPluginManager.java:635)
	at nextflow.plugin.PluginsFacade.getExtensions(PluginsFacade.groovy:329)
	at nextflow.plugin.Plugins.getExtensions(Plugins.groovy:61)
	at nextflow.config.ConfigValidator.loadPluginScopes(ConfigValidator.groovy:75)
	at nextflow.config.ConfigValidator.<init>(ConfigValidator.groovy:70)
	at nextflow.cli.CmdRun.run(CmdRun.groovy:405)
	at nextflow.cli.Launcher.run(Launcher.groovy:526)
	at nextflow.cli.Launcher.main(Launcher.groovy:686)
	at org.pf4j.PluginClassLoader.loadClass(PluginClassLoader.java:169)
and by tons i mean hundreds of thousands of lines. Anyone seen this?
🫠 1
m
I have not noticed this, which Nextflow version are you using?
I hate having such warning messages with a very strong force
During my PhD, I somehow created a log file with a single warning message repeating over and over and over, until it reached a critical size. Since then I pay a lot of attention to warning messages, and try to remove as much as I can.
m
Nothing like running out of local disk because of logging 🙂
m
I wish it was a local disk
m
😆
Dear IT admins, please find enclosed my apology letter for crashing your NAS with logging noise.
m
I found a tweet I made about this story some years ago: https://x.com/gau/status/1298971672402374660
😆 1
m
we've all been there. I used to run support and analysis for a database product. There are infinite ways to break the A in CAP. I'll leave it at that.
🙏 1
m
That's what I always say, we have all made mistakes, let's just try to be better
m
Will move discussion of this topic to the #C04QH4Y6ZMK thread so it's not a split convo.
👍 1
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