Java error running interproscan

usegalaxy.eu support
,
1

I’m trying to run the interproscan tool but I get this error:

Picked up _JAVA_OPTIONS: -Duser.home=/data/jwd08/main/000/101/981/101981135/home
log4j:WARN No appenders could be found for logger (org.apache.activemq.broker.BrokerService).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.

I ran it successfully on 11 may but today I’m getting this error. Should I just wait a while and try again?

2

Hi @Michael_Thon

The UseGalaxy.eu server might have been still bringing up services earlier. → Galaxy Europe downtime: ongoing maintenance work Tue, May 12

Have you tried again now? I’ll also run a quick test to see how this is working. We can let them know if this seems to be still outstanding. :slight_smile:

3

Hi @jennaj - I just tried again, but the job still failed with the same log4j error…

4

Hi @jennaj I think I found a partial solution. There is an option in interproscan to use 3 applications that are restricted to non-commercial use. If I set that option to ‘yes’ then I get the log4j error. I just set it to ‘no’ and now interproscan seems to be running. Later I’ll try some previous tool versions to see if the bug is in them or not.

5

Hi @Michael_Thon

Ok, thanks for explaining more, this makes sense. For some reason I thought this was happening for prior runs that were successful! I should have noticed that it was for a new job and using the restricted index choices. There is usually more in the logs, but maybe that was dropped.

How this tool works is explained in topics like interproscan

This is likely the clearest explanation. All of the UseGalaxy public servers will work the same with respect to the permissions. → Interproscan log4j error - #3 by igor

In short, the tool form is designed to support the inclusion of a license, but we can’t do that on the public servers (and don’t even have the other reference data indexed!). Instead, using a private Galaxy would be needed. You can work at the public site and your own together. This was discussed for another tool recently if interested (KEGG indexes have licensing restrictions too!) . → KOfam database (HMM profiles of KEGG Orthologs): licensing and KEGG - #2 by jennaj

Does this make sense? Are you able to use the unrestricted indexes?

Thanks! :slight_smile: