Re: [Nelsonlab-analysis] Picard MarkDuplicates error--anybody have any ideas?

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Mike, 

How are you splitting the bam files? This is the way that I usually do it.

  samtools view -h ./input.bam chr3_random | samtools view -bS - > ./output.bam

-bret

On Sun, May 16, 2010 at 08:11:35PM -0700, Michael James Clark wrote:
> Here's a clue, maybe. To narrow in on the region, I was going to index one 
> of the files. When I ran samtools index, I got a couple of errors on one of 
> the files that didn't work:
>
> -bash- samtools index 1102T.LMP.chr3_random.bam
> [bam_header_read] EOF marker is absent.
> [bam_index_core] truncated file? Continue anyway. (-4)
>
> When I ran samtools index on one of the files that worked, I didn't get that error. Not really sure why the file would be "truncated" when others from the same process aren't.
>
>
>
> On 5/16/2010 7:13 PM, Bret Harry wrote:
>> Mike,
>>
>> I have not seen this error before, how long does it take to reproduce this for 1102T.LMP.rmdup.chrY.bam ? I think I would start by further splitting up the BAM file until I got to the smallest possible file size that caused a crash. It's unclear if Picard is crashing because of what's *in* the bam file, or because of the *size* of the bam file.
>>
>> -bret
>>
>> On Sun, May 16, 2010 at 04:51:59PM -0700, Michael James Clark wrote:
>>    
>>> Hi guys,
>>> I've been trying to get 1102's tumor to run through Picard
>>> MarkDuplicates for two weeks now. Resorted to splitting the whole genome
>>> file up by chromosome and trying to run that. SOME of it has worked, but
>>> some of them crashed with the following error:
>>>
>>>    /usr/java/latest/bin/java -Xmx6G -jar
>>> /share/apps/picard-tools-1.19/MarkDuplicates.jar I=1102T.LMP.chrY.bam
>>> O=1102T.LMP.rmdup.chrY.bam M=1102T.LMP.rmdup.chrY.metrics
>>> TMP_DIR=tmp.files/ REMOVE_DUPLICATES=TRUE VALIDATION_STRINGENCY=SILENT
>>> MAX_RECORDS_IN_RAM=8000000
>>> [Sun May 16 16:32:46 PDT 2010] net.sf.picard.sam.MarkDuplicates
>>> INPUT=1102T.LMP.chrY.bam OUTPUT=1102T.LMP.rmdup.chrY.bam
>>> METRICS_FILE=1102T.LMP.rmdup.chrY.metrics REMOVE_DUPLICATES=true
>>> TMP_DIR=tmp.files VALIDATION_STRINGENCY=SILENT
>>> MAX_RECORDS_IN_RAM=8000000    ASSUME_SORTED=false
>>> MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000
>>> READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*
>>> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=INFO QUIET=false
>>> COMPRESSION_LEVEL=5
>>> INFO    2010-05-16 16:32:46     MarkDuplicates  Start of doWork
>>> freeMemory: 8658104; totalMemory: 9109504; maxMemory: 5726666752
>>> INFO    2010-05-16 16:32:46     MarkDuplicates  Reading input file and
>>> constructing read end information.
>>> INFO    2010-05-16 16:32:46     MarkDuplicates  Will retain up to
>>> 22724868 data points before spilling to disk.
>>> INFO    2010-05-16 16:33:07     MarkDuplicates  Read 1000000 records.
>>> Tracking 2526 as yet unmatched pairs. 2526 records in RAM.  Last
>>> sequence index: 23
>>> INFO    2010-05-16 16:33:17     MarkDuplicates  Read 2000000 records.
>>> Tracking 6482 as yet unmatched pairs. 6482 records in RAM.  Last
>>> sequence index: 23
>>> INFO    2010-05-16 16:33:27     MarkDuplicates  Read 3000000 records.
>>> Tracking 10160 as yet unmatched pairs. 10160 records in RAM.  Last
>>> sequence index: 23
>>> INFO    2010-05-16 16:33:36     MarkDuplicates  Read 4000000 records.
>>> Tracking 68510 as yet unmatched pairs. 68510 records in RAM.  Last
>>> sequence index: 23
>>> INFO    2010-05-16 16:33:46     MarkDuplicates  Read 5000000 records.
>>> Tracking 75782 as yet unmatched pairs. 75782 records in RAM.  Last
>>> sequence index: 23
>>> INFO    2010-05-16 16:33:55     MarkDuplicates  Read 6000000 records.
>>> Tracking 97889 as yet unmatched pairs. 97889 records in RAM.  Last
>>> sequence index: 23
>>> INFO    2010-05-16 16:34:03     MarkDuplicates  Read 7000000 records.
>>> Tracking 60997 as yet unmatched pairs. 60997 records in RAM.  Last
>>> sequence index: 23
>>> INFO    2010-05-16 16:34:13     MarkDuplicates  Read 8000000 records.
>>> Tracking 61125 as yet unmatched pairs. 61125 records in RAM.  Last
>>> sequence index: 23
>>> INFO    2010-05-16 16:34:22     MarkDuplicates  Read 9000000 records.
>>> Tracking 60597 as yet unmatched pairs. 60597 records in RAM.  Last
>>> sequence index: 23
>>> INFO    2010-05-16 16:34:33     MarkDuplicates  Read 10000000 records.
>>> Tracking 58306 as yet unmatched pairs. 58306 records in RAM.  Last
>>> sequence index: 23
>>> INFO    2010-05-16 16:34:41     MarkDuplicates  Read 11000000 records.
>>> Tracking 55412 as yet unmatched pairs. 55412 records in RAM.  Last
>>> sequence index: 23
>>> INFO    2010-05-16 16:34:53     MarkDuplicates  Read 12000000 records.
>>> Tracking 51336 as yet unmatched pairs. 51336 records in RAM.  Last
>>> sequence index: 23
>>> INFO    2010-05-16 16:35:02     MarkDuplicates  Read 13000000 records.
>>> Tracking 13051 as yet unmatched pairs. 13051 records in RAM.  Last
>>> sequence index: 23
>>> [Sun May 16 16:35:04 PDT 2010] net.sf.picard.sam.MarkDuplicates done.
>>> Runtime.totalMemory()=2987982848
>>> Exception in thread "main" net.sf.samtools.FileTruncatedException:
>>> Premature end of file
>>>           at
>>> net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:290)
>>>           at
>>> net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:100)
>>>           at
>>> net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:169)
>>>           at java.io.DataInputStream.read(DataInputStream.java:132)
>>>           at
>>> net.sf.samtools.util.BinaryCodec.readBytesOrFewer(BinaryCodec.java:394)
>>>           at net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:371)
>>>           at net.sf.samtools.util.BinaryCodec.readBytes(BinaryCodec.java:357)
>>>           at net.sf.samtools.BAMRecordCodec.decode(BAMRecordCodec.java:182)
>>>           at
>>> net.sf.samtools.BAMFileReader$BAMFileIterator.getNextRecord(BAMFileReader.java:397)
>>>           at
>>> net.sf.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:373)
>>>           at
>>> net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:363)
>>>           at
>>> net.sf.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:330)
>>>           at
>>> net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:261)
>>>           at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:112)
>>>           at
>>> net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150)
>>>           at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:96)
>>>
>>> It crashes immediately upon saying "net.sf.picard.sam.MarkDuplicates
>>> done." with this Premature end of file error. Anyone have any ideas how
>>> to get around this and get it to work?
>>>
>>> Thanks,
>>> Mike
>>>
>>> ------------------------------------------------------------------------------
>>>
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