Trimmomatic randomly fails

[talnor]

Describe the bug Trimming with trimmomatic sometimes (seemingly) randomly fails. It has been observed that runs that fail may complete without errors when running the same command again. This has been occuring since fixing the microSALT installation issues in PR #142.

Expected behavior Trimmomatic should complete without errors.

Screenshots

# A fatal error has been detected by the Java Runtime Environment:  
#  
# SIGILL (0x4) at pc=0x00007f51c8695367, pid=5762, tid=5819  
#  
# JRE version: OpenJDK Runtime Environment (11.0.2+7) (build 11.0.2+7)  
# Java VM: OpenJDK 64-Bit Server VM (11.0.2+7, mixed mode, tiered, compressed oops, g1 gc, linux-amd64)  
# Problematic frame:  
# J 784 c2 org.usadellab.trimmomatic.trim.IlluminaClippingTrimmer$IlluminaLongClippingSeq.readsSeqCompare(Lorg/usadellab/trimmomatic/fastq/FastqRecord;)Ljava/lang/Integer; (306 bytes) @ 0x00007f51c8695367 [0x00007f51c8693e40+0x0000000000001527]  
#  
# No core dump will be written. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again  
#  
# If you would like to submit a bug report, please visit:  
# https://github.com/AdoptOpenJDK/openjdk-build/issues  
#

Software version:

• Trimmomatic version 0.39
• openjdk version 11.0.1
• microSALT version 3.3.4 (4d369b0)

[talnor]

Should be solved. Closing.