Investigate GATK error message with docker --network none

[GATKSupportTeam]

This error message occurs when removing the network when running GATK in a docker container. GATK tools still run to completion, but the error message is disruptive.

$> docker run --rm --network none broadinstitute/gatk gatk -version

2022-08-03 20:37:23,349 main ERROR Could not determine local host name java.net.UnknownHostException: de2c81c88ddc: de2c81c88ddc: Temporary failure in name resolution
at java.net.InetAddress.getLocalHost(InetAddress.java:1506)
at org.apache.logging.log4j.core.util.NetUtils.getLocalHostname(NetUtils.java:54)
at org.apache.logging.log4j.core.LoggerContext.lambda$setConfiguration$0(LoggerContext.java:620)
at java.util.concurrent.ConcurrentHashMap.computeIfAbsent(ConcurrentHashMap.java:1660)
at org.apache.logging.log4j.core.LoggerContext.setConfiguration(LoggerContext.java:620)
at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:699)
at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:716)
at org.apache.logging.log4j.core.LoggerContext.start(LoggerContext.java:270)
at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:155)
at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:47)
at org.apache.logging.log4j.LogManager.getContext(LogManager.java:196)
at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:599)
at org.broadinstitute.hellbender.utils.Utils.<clinit>(Utils.java:72)
at org.broadinstitute.hellbender.Main.<clinit>(Main.java:45)
Caused by: java.net.UnknownHostException: de2c81c88ddc: Temporary failure in name resolution
at java.net.Inet4AddressImpl.lookupAllHostAddr(Native Method)
at java.net.InetAddress$2.lookupAllHostAddr(InetAddress.java:929)
at java.net.InetAddress.getAddressesFromNameService(InetAddress.java:1324)
at java.net.InetAddress.getLocalHost(InetAddress.java:1501)
...13 more

The Genome Analysis Toolkit (GATK) v4.2.6.1
HTSJDK Version: 2.24.1
Picard Version: 2.27.1
Using GATK jar /gatk/gatk-package-4.2.6.1-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /gatk/gatk-package-4.2.6.1-local.jar -version

This request was created from a contribution made by Pryce Turner on July 29, 2022 03:44 UTC.

Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360078378372--Could-not-determine-local-host-name-#community_comment_7692552841755

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Hey 417227834892,

Were you ever able to solve this? I'm running into the same issue with HaplotypeCaller. It still runs, but the error output is potentially disruptive.

Thanks!

(created from Zendesk ticket #292152)
gz#292152

[pryce-turner]

Just wanted to highlight something from the thread that's hopefully salient: this issue does not occur when using Podman with exactly the same image/params.

[droazen]

This appears to be a log4j issue that we don't have direct control over, unfortunately.

[lbergelson]

I opened a log4j issue. Maybe someone will fix it in the future. https://issues.apache.org/jira/browse/LOG4J2-3602