Interproscan error while running metawibele characterize

Microbial community profiling MetaWIBELE
1

Hi Yancong,

Thank you for your previous help. The latest version v0.4.8 is working with Seqkit.

Unfortunately, I encountered an error while running metawibele characterize. As far I figured out, interproscan is the problem.

The error message from domain_motif_annotation/InterProScan/split1/split1.interproscan.err is

26/01/2024 13:40:41:064 Welcome to InterProScan-5.59-91.0
26/01/2024 13:40:41:064 Running InterProScan v5 in STANDALONE mode... on Linux
26/01/2024 13:40:45:457 RunID: gnc-1_20240126_134045310_jja
26/01/2024 13:40:57:433 Loading file /home/gihyeon/Pipelines/Metawibele/GEN001_201/temp/split1/GEN001_201_genecatalogs.cen>
26/01/2024 13:40:57:434 Running the following analyses:
[AntiFam-7.0,CDD-3.18,Coils-2.2.1,FunFam-4.3.0,Gene3D-4.3.0,Hamap-2021_04,MobiDBLite-2.0,PANTHER-17.0,Pfam-35.0,PIRSF-3.10>
Pre-calculated match lookup service DISABLED.  Please wait for match calculations to complete...

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "ActiveMQ Broker[localhost] Sched>

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "main"

Exception: java.lang.OutOfMemoryError thrown from the UncaughtExceptionHandler in thread "amqEmbeddedWorkerJmsContainer-2"

So, I tried changing worker.number.of.embedded.workers and worker.maxnumber.of.embedded.workers to 4, and worker.command=java -Xms32m -Xmx4096m -jar interproscan-5.jar in interproscan.properties.

But, those changes did not work.

Do you have any idea?

Thanks,
Gihyeon

2

Hi Gihyeon,

Did you check whether InterProScan works if you run it separately? E.g.
interproscan.sh -i your_proteins.fasta If not, you might want to ask help from its developers through this thread: Issues · ebi-pf-team/interproscan · GitHub

If InterProScan works separately but fails in MetaWIBELE, it is possible that you got your computational resource limit when running MetaWIBELE. MetaWIBELE may perform multiple InterProScan runs simultaneously based on your configurations, resulting in out-of-memory issues. In this case, you could adjust your running configs to reduce the number of multi-running InterProScan jobs, e.g. running parameters --local-jobs --threads for metawibele characterize; config parameters split_number in your metawibele.cfg

Thanks!
Yancong