Dear Samtools-list,
Recently, I used Picardtools/MarkDuplicates as following:
java -Djava.io.tmpdir=/data/mira0501/agilentfastq/nonmulti/ -Xmx4g -Xms4g
-jar /home/mira0501/apps/picard-tools-1.119/MarkDuplicates.jar
MAX_FILE_HANDLES_FOR_READ_END
S_MAP=1000 I=e_ptgene.sorted.bam O=e_ptgene.dedup.bam
M=e_ptgenedup.metrics AS=true VALIDATION_STRINGENCY=LENIENT
After 45 mins, the error message showed:
___________________________________________________________________
.......
INFO 2014-09-29 14:53:30 MarkDuplicates Tracking 1004938 as yet
unmatched pairs. 89 records in RAM.
INFO 2014-09-29 14:56:08 MarkDuplicates Read 12,000,000
records. Elapsed time: 00:41:57s. Time for last 1,000,000: 158s. Last
read position: scaffold3685
03:22,683
INFO 2014-09-29 14:56:08 MarkDuplicates Tracking 1078120 as yet
unmatched pairs. 36 records in RAM.
[Mon Sep 29 14:57:41 CDT 2014] picard.sam.MarkDuplicates done. Elapsed
time: 43.51 minutes.
Runtime.totalMemory()=3818389504
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMException: Exception closing
FileOutputStream for
/data/mira0501/agilentfastq/nonmulti/mira0501/CSPI.5751822609546779855.t
mp/27421.tmp
at
htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.finalizeValue(FileAppendStreamLRUCache.java:74)
at
htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.finalizeValue(FileAppendStreamLRUCache.java:49)
at
htsjdk.samtools.util.ResourceLimitedMap$1.removeEldestEntry(ResourceLimitedMap.java:59)
at java.util.LinkedHashMap.addEntry(LinkedHashMap.java:431)
at java.util.HashMap.put(HashMap.java:509)
at
htsjdk.samtools.util.ResourceLimitedMap.get(ResourceLimitedMap.java:76)
at
htsjdk.samtools.CoordinateSortedPairInfoMap.getOutputStreamForSequence(CoordinateSortedPairInfoMap.java:180)
at
htsjdk.samtools.CoordinateSortedPairInfoMap.put(CoordinateSortedPairInfoMap.java:164)
at picard.sam.DiskReadEndsMap.put(DiskReadEndsMap.java:67)
at
picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:449)
at picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:177)
at
picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183)
at picard.sam.MarkDuplicates.main(MarkDuplicates.java:161)
Caused by: java.io.IOException: Input/output error
at java.io.FileOutputStream.close0(Native Method)
at java.io.FileOutputStream.close(FileOutputStream.java:393)
at java.io.FilterOutputStream.close(FilterOutputStream.java:160)
at
htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.finalizeValue(FileAppendStreamLRUCache.java:71)
... 12 more
__________________________________________________________________
Then I tried it again,and I did not change anything in the command. This
time, it lasted longer, after 1hour, it reported the error:
_____________________________________________________________
......
INFO 2014-09-29 21:14:59 MarkDuplicates Tracking 1509035 as yet
unmatched pairs. 119 records in RAM.
INFO 2014-09-29 21:15:37 MarkDuplicates Read 45,000,000
records. Elapsed time: 01:43:10s. Time for last 1,000,000: 38s. Last
read position: tscaffold375
9:199,308
INFO 2014-09-29 21:15:37 MarkDuplicates Tracking 1476529 as yet
unmatched pairs. 78 records in RAM.
[Mon Sep 29 21:17:31 CDT 2014] picard.sam.MarkDuplicates done. Elapsed
time: 105.41 minutes.
Runtime.totalMemory()=3922722816
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" htsjdk.samtools.SAMException: Exception closing
FileOutputStream for
/data/mira0501/agilentfastq/nonmulti/mira0501/CSPI.2781500592681706581.t
mp/29668.tmp
at
htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.finalizeValue(FileAppendStreamLRUCache.java:74)
at
htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.finalizeValue(FileAppendStreamLRUCache.java:49)
at
htsjdk.samtools.util.ResourceLimitedMap$1.removeEldestEntry(ResourceLimitedMap.java:59)
at java.util.LinkedHashMap.addEntry(LinkedHashMap.java:431)
at java.util.HashMap.put(HashMap.java:509)
at
htsjdk.samtools.util.ResourceLimitedMap.get(ResourceLimitedMap.java:76)
at
htsjdk.samtools.CoordinateSortedPairInfoMap.getOutputStreamForSequence(CoordinateSortedPairInfoMap.java:180)
at
htsjdk.samtools.CoordinateSortedPairInfoMap.put(CoordinateSortedPairInfoMap.java:164)
at picard.sam.DiskReadEndsMap.put(DiskReadEndsMap.java:67)
at
picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:449)
at picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:177)
at
picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183)
at picard.sam.MarkDuplicates.main(MarkDuplicates.java:161)
Caused by: java.io.IOException: Input/output error
at java.io.FileOutputStream.close0(Native Method)
at java.io.FileOutputStream.close(FileOutputStream.java:393)
at java.io.FilterOutputStream.close(FilterOutputStream.java:160)
at
htsjdk.samtools.util.FileAppendStreamLRUCache$Functor.finalizeValue(FileAppendStreamLRUCache.java:71)
... 12 more
_________________________________________________________
Dear fellow picard users, could you advise what should I do for "Exception
in thread "main" htsjdk.samtools.SAMException: Exception closing
FileOutputStream" and "java.io.IOException: Input/output error",please?
Thanks very much!
Mengmeng
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