Hi Alec, Thank you very much for your reply. I have the thread dump, it looks like some of the threads are locked or waiting on a condition. Could you (or someone else) please guide me on how I should resolve this?
Thank you, Stuti *Attached: thread dump* 2014-11-25 22:29:30 Full thread dump Java HotSpot(TM) 64-Bit Server VM (25.25-b02 mixed mode): "Attach Listener" #18 daemon prio=9 os_prio=0 tid=0x00007f48e4001000 nid=0x3de2 waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE "Service Thread" #17 daemon prio=9 os_prio=0 tid=0x00007f49802d4000 nid=0x8ac runnable [0x0000000000000000] java.lang.Thread.State: RUNNABLE "C1 CompilerThread11" #16 daemon prio=9 os_prio=0 tid=0x00007f49802c7000 nid=0x8ab waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE "C1 CompilerThread10" #15 daemon prio=9 os_prio=0 tid=0x00007f49802c5000 nid=0x8aa waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE "C1 CompilerThread9" #14 daemon prio=9 os_prio=0 tid=0x00007f49802c2800 nid=0x8a9 waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE "C1 CompilerThread8" #13 daemon prio=9 os_prio=0 tid=0x00007f49802c0800 nid=0x8a8 waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE "C2 CompilerThread7" #12 daemon prio=9 os_prio=0 tid=0x00007f49802be800 nid=0x8a7 waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE "C2 CompilerThread6" #11 daemon prio=9 os_prio=0 tid=0x00007f49802bc000 nid=0x8a6 waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE "C2 CompilerThread5" #10 daemon prio=9 os_prio=0 tid=0x00007f49802ba000 nid=0x8a5 waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE "C2 CompilerThread4" #9 daemon prio=9 os_prio=0 tid=0x00007f49802b0000 nid=0x8a4 waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE "C2 CompilerThread3" #8 daemon prio=9 os_prio=0 tid=0x00007f49802ab800 nid=0x8a3 waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE "C2 CompilerThread2" #7 daemon prio=9 os_prio=0 tid=0x00007f49802a9800 nid=0x8a2 waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE "C2 CompilerThread1" #6 daemon prio=9 os_prio=0 tid=0x00007f49802a7800 nid=0x8a1 waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE "C2 CompilerThread0" #5 daemon prio=9 os_prio=0 tid=0x00007f49802a4800 nid=0x8a0 waiting on condition [0x0000000000000000] java.lang.Thread.State: RUNNABLE "Signal Dispatcher" #4 daemon prio=9 os_prio=0 tid=0x00007f49802a2800 nid=0x89f runnable [0x0000000000000000] java.lang.Thread.State: RUNNABLE "Finalizer" #3 daemon prio=8 os_prio=0 tid=0x00007f4980275800 nid=0x89e in Object.wait() [0x00007f493a3e2000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) - waiting on <0x0000000080057158> (a java.lang.ref.ReferenceQueue$Lock) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:142) - locked <0x0000000080057158> (a java.lang.ref.ReferenceQueue$Lock) at java.lang.ref.ReferenceQueue.remove(ReferenceQueue.java:158) at java.lang.ref.Finalizer$FinalizerThread.run(Finalizer.java:209) "Reference Handler" #2 daemon prio=10 os_prio=0 tid=0x00007f4980273800 nid=0x89d in Object.wait() [0x00007f493a4e3000] java.lang.Thread.State: WAITING (on object monitor) at java.lang.Object.wait(Native Method) - waiting on <0x0000000080058fb8> (a java.lang.ref.Reference$Lock) at java.lang.Object.wait(Object.java:502) at java.lang.ref.Reference$ReferenceHandler.run(Reference.java:157) - locked <0x0000000080058fb8> (a java.lang.ref.Reference$Lock) "main" #1 prio=5 os_prio=0 tid=0x00007f498000a000 nid=0x88e runnable [0x00007f4986f0f000] java.lang.Thread.State: RUNNABLE at java.io.FileOutputStream.writeBytes(Native Method) at java.io.FileOutputStream.write(FileOutputStream.java:315) at java.io.BufferedOutputStream.write(BufferedOutputStream.java:122) - locked <0x0000000080058da0> (a java.io.BufferedOutputStream) at java.io.PrintStream.write(PrintStream.java:480) - locked <0x0000000080058d80> (a java.io.PrintStream) at sun.nio.cs.StreamEncoder.writeBytes(StreamEncoder.java:221) at sun.nio.cs.StreamEncoder.implFlushBuffer(StreamEncoder.java:291) at sun.nio.cs.StreamEncoder.flushBuffer(StreamEncoder.java:104) - locked <0x0000000080058ec0> (a java.io.OutputStreamWriter) at java.io.OutputStreamWriter.flushBuffer(OutputStreamWriter.java:185) at java.io.PrintStream.write(PrintStream.java:527) - locked <0x0000000080058d80> (a java.io.PrintStream) at java.io.PrintStream.print(PrintStream.java:669) at java.io.PrintStream.println(PrintStream.java:806) - locked <0x0000000080058d80> (a java.io.PrintStream) at htsjdk.samtools.util.Log.emit(Log.java:123) at htsjdk.samtools.util.Log.info(Log.java:203) at htsjdk.samtools.util.ProgressLogger.record(ProgressLogger.java:82) - eliminated <0x00000000800572f0> (a htsjdk.samtools.util.ProgressLogger) at htsjdk.samtools.util.ProgressLogger.record(ProgressLogger.java:100) - locked <0x00000000800572f0> (a htsjdk.samtools.util.ProgressLogger) at picard.sam.SamToFastq.doWork(SamToFastq.java:185) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:187) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:89) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:99) "VM Thread" os_prio=0 tid=0x00007f498026c800 nid=0x89c runnable "GC task thread#0 (ParallelGC)" os_prio=0 tid=0x00007f498001f000 nid=0x88f runnable "GC task thread#1 (ParallelGC)" os_prio=0 tid=0x00007f4980021000 nid=0x890 runnable "GC task thread#2 (ParallelGC)" os_prio=0 tid=0x00007f4980022800 nid=0x891 runnable "GC task thread#3 (ParallelGC)" os_prio=0 tid=0x00007f4980024800 nid=0x892 runnable "GC task thread#4 (ParallelGC)" os_prio=0 tid=0x00007f4980026000 nid=0x893 runnable "GC task thread#5 (ParallelGC)" os_prio=0 tid=0x00007f4980028000 nid=0x894 runnable "GC task thread#6 (ParallelGC)" os_prio=0 tid=0x00007f4980029800 nid=0x895 runnable "GC task thread#7 (ParallelGC)" os_prio=0 tid=0x00007f498002b800 nid=0x896 runnable "GC task thread#8 (ParallelGC)" os_prio=0 tid=0x00007f498002d000 nid=0x897 runnable "GC task thread#9 (ParallelGC)" os_prio=0 tid=0x00007f498002f000 nid=0x898 runnable "GC task thread#10 (ParallelGC)" os_prio=0 tid=0x00007f4980030800 nid=0x899 runnable "GC task thread#11 (ParallelGC)" os_prio=0 tid=0x00007f4980032800 nid=0x89a runnable "GC task thread#12 (ParallelGC)" os_prio=0 tid=0x00007f4980034000 nid=0x89b runnable "VM Periodic Task Thread" os_prio=0 tid=0x00007f49802df000 nid=0x8ad waiting on condition JNI global references: 50 On 25 November 2014 at 16:22, Alec Wysoker <al...@broadinstitute.org> wrote: > Hi Stuti, > > In order to diagnose the problem, try the following: > > 1. Determine the process ID of the hung job by logging onto the > machine where the job is running and execute 'jps -lv' > 2. Get a thread dump of the hung process with 'jstack <process-id>' > > If it isn't obvious from looking at the thread dump what the problem is, > then send it to the list and someone should be able to figure it out. > > -Alec > On 11/25/14, 12:49 PM, Stuti Agrawal wrote: > > Hi, > > I am trying to use Picard - SamToFastq for the cell line dataset for > TCGA, which is ~200G BAM file. However, when I run the command, the > fastq.gz files are created of 14G each after which Picard just stalls. The > java virtual machine goes into a sleep mode, the job is still running/alive > but there is no progress. > > I am running this on a 16 core VM with 48G memory and there is nothing > else running on this machine. Is there a way I can run this so that the job > completes? > > Thank you, > Stuti Agrawal > > This is the command I have used: > *java* -Xms2G -Xmx30G -jar > /home/ubuntu/software/picard-tools-1.124/picard.jar SamToFastq > VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=7500000 > INPUT=/mnt/cinder/SCRATCH/data/tcga/dataset/G15511.HCC1143.1.bam > FASTQ=/mnt/cinder/SCRATCH/data/tcga/dataset/ad3d4757-f358-40a3-9d92-742463a95e88_1.fastq.gz > SECOND_END_FASTQ=/mnt/cinder/SCRATCH/data/tcga/dataset/ad3d4757-f358-40a3-9d92-742463a95e88_2.fastq.gz > > -- > *Stuti Agrawal* > > > > > > ------------------------------------------------------------------------------ > Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server > from Actuate! Instantly Supercharge Your Business Reports and Dashboards > with Interactivity, Sharing, Native Excel Exports, App Integration & more > Get technology previously reserved for billion-dollar corporations, > FREEhttp://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk > > > > _______________________________________________ > Samtools-help mailing > listSamtools-help@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/samtools-help > > > -- *Stuti Agrawal*
thread_dump
Description: Binary data
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