Failed to spawn exec helper errors with java 13.0.1

[hyphaltip]

Here are errors and a workaround when running under java 13.0.1. Maybe add this to the known issues page for iprscan?

java -version
openjdk version "13.0.1" 2019-10-15
OpenJDK Runtime Environment (build 13.0.1+9)
OpenJDK 64-Bit Server VM (build 13.0.1+9, mixed mode, sharing)

I get these error messages throughout:

java.io.IOException: Cannot run program "/bin/bash": error=0, Failed to exec spawn helper.
Caused by: java.io.IOException: Cannot run program "bin/blast/ncbi-blast-2.10.1+/rpsblast": error=0, Failed to exec spawn helper.
Caused by: java.io.IOException: error=0, Failed to exec spawn helper.
Caused by: java.io.IOException: Cannot run program "bin/blast/ncbi-blast-2.10.1+/rpsblast": error=0, Failed to exec spawn helper.
Caused by: java.io.IOException: error=0, Failed to exec spawn helper.
Caused by: java.io.IOException: Cannot run program "perl": error=0, Failed to exec spawn helper.
Caused by: java.io.IOException: error=0, Failed to exec spawn helper.
Caused by: java.io.IOException: Cannot run program "perl": error=0, Failed to exec spawn helper.
Caused by: java.io.IOException: error=0, Failed to exec spawn helper.
Caused by: java.io.IOException: Cannot run program "bin/prosite/ps_scan.pl": error=0, Failed to exec spawn helper.

Googled for Failed to exec spawn helper and found:
https://stackoverflow.com/questions/61301818/java-failed-to-exec-spawn-helper-error-since-moving-to-java-14-on-linux

In the last part of answers

An alternative workaround is to add the following java option:

-Djdk.lang.Process.launchMechanism=vfork

I added that bit to the /opt/linux/centos/7.x/x86_64/pkgs/interproscan/5.48-83.0/interproscan.sh
so the end of that script goes from:

"$JAVA" \
-XX:+UseParallelGC -XX:ParallelGCThreads=4  \
 -Xms1028M -Xmx6072M \
-jar  interproscan-5.jar $@ -u $USER_DIR

to

"$JAVA" \
-XX:+UseParallelGC -XX:ParallelGCThreads=4  \
 -Xms1028M -Xmx6072M -Djdk.lang.Process.launchMechanism=vfork \
-jar  interproscan-5.jar $@ -u $USER_DIR

[hyphaltip]

An example logfile error for the spawn process:
proteins_1.ipr.log

[gsn7]

I have now tested interproscan on java 13.0.2+8, java 15.0.2+7 and java 16+36 and did not get the spawn errors. So this bug in java might have been fixed