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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
gned.dedupped.bamoutput.metrics

and hs_err_pid41340.log is attached.

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Answers

  • akovalskakovalsk Member, Broadie, Moderator admin

    Hi @erubin1967

    This may also be a result of using an outdated version of PICARD. It is recommended that you update to the latest PICARD version. If any of these issues persist, please repost your question in the new forum where we have recently moved. Thank you!

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