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Why am I getting this error massage?
I am running PICARD as follows. The program died on me after almost finishing. I ran the following command:
bash tmp2.bash > & stdout.tmp2.bash &
after setting the environmental variable for Java memory:
echo $_JAVA_OPTIONS -Xmx600g -Xms500g
Here is the end of the log:
INFO 2019-12-29 21:55:07 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:15:09s. Time for last 10,00
0,000: 65s. Last read position: NW_021160023.1:493,493
INFO 2019-12-29 21:56:15 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:16:16s. Time for last 10,00
0,000: 67s. Last read position: NW_021160023.1:493,623
# A fatal error has been detected by the Java Runtime Environment: # SIGSEGV (0xb) at pc=0x00007f6f135d5d27, pid=41340, tid=0x00007f6f1013c700 # JRE version: Java(TM) SE Runtime Environment (8.0_131-b11) (build 1.8.0_131-b11) Java VM: Java HotSpot(TM) 64-Bit Server VM (25.131-b11 mixed mode linux-amd64 ) Problematic frame: V [libjvm.so+0x649d27] InstanceKlass::oop_follow_contents(ParCompactionManager*, oopDesc*)+0x187 # Failed to write core dump. Core dumps have been disabled. To enable core dumping, try "ulimit -c unlimited" before starting Java again
# An error report file with more information is saved as: /gpfs0/biores/users/erubin/Haviv/Analysis5/hs_err_pid41340.log # If you would like to submit a bug report, please visit: http://bugreport.java.com/bugreport/crash.jsp #
tmp2.bash: line 1: 41340 Aborted /gpfs0/biores/home/erubin/jdk/jdk1.8.0_131/bin/java -jar /gpfs0/biores/users
/erubin/jars/picard-2.11.0.jar MarkDuplicates I=Data/RNAseq/5-1524_S1_merged_R1_001.Aligned.sorted.bam O=Data/RNAseq/5-1524_S
1_merged_R1_001.Aligned.dedupped.bam CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT M=Data/RNAseq/5-1524_S1_merged_R1_001.Ali
and hs_err_pid41340.log is attached.