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
<http://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
<mailto: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_
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