Hey Antonio,
we are tracking your issue here:
https://github.com/broadinstitute/picard/issues/136
N
On Mon, Nov 24, 2014 at 10:27 AM, antonio agraz <
antonio.agraz.bio...@gmail.com> wrote:
>
> Good afternoon Nils.
>
> I attach ouputs and log for ValidateSamFile from input BAM to
> MarkDuplicates.
>
> Thanks. Antonio M. Agraz
>
> 2014-11-24 15:28 GMT+01:00 Nils Homer <nho...@broadinstitute.org>:
>
>> Hey Antonio,
>>
>> could you run ValidateSamFile on the input BAM to MarkDuplicates? If you
>> have a small test case on which we can reproduce, please send it along,
>>
>> N
>>
>> On Mon, Nov 24, 2014 at 5:14 AM, antonio agraz <
>> antonio.agraz.bio...@gmail.com> wrote:
>>
>>> Good afternoon. I send you this mail due to dubts using Picard.
>>>
>>> We use Picard/CleanSmar.jar:
>>> java -Xmx4g -jar $Picard_jarFolder/CleanSam.jar INPUT=$sample
>>> OUTPUT=$clean_picard VALIDATION_STRINGENCY=LENIENT 2>$log_clean_picard"
>>>
>>> Later we use fixmate a sort by samtools.
>>> but when we use the next step:
>>>
>>> java -Xmx2g -jar $Picard_jarFolder/MarkDuplicates.jar
>>> INPUT=$sorted1_samtools_bam OUTPUT=$sorted_picard_marked_bam TMP_DIR=./
>>> METRICS_FILE=$log_duplicate_metrics REMOVE_DUPLICATES=false
>>> ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
>>> 2>$log_picard_marked_bam"
>>>
>>> We have the next problem and we dont know why, if we had used CleanSam
>>> (which it is supposed to
>>>
>>> Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference
>>> alignments and setting MAPQ to 0 for unmapped reads)
>>>
>>> [Thu Nov 13 12:43:12 CET 2014] net.sf.picard.sam.MarkDuplicates done.
>>> Elapsed time: 10,13 minutes.
>>> Runtime.totalMemory()=1691418624
>>> Exception in thread "main" net.sf.samtools.SAMException: Exception when
>>> processing alignment for BAM index HS12_10750:8:2310:1400:98064#42 1/2 75b
>>> unmapped read.
>>> at net.sf.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:112)
>>> at net.sf.samtools
>>> .SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:168)
>>> at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:208)
>>> at net.sf.picard
>>> .cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
>>> at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:106)
>>> Caused by: net.sf.samtools.SAMException: Exception creating BAM index
>>> for record HS12_10750:8:2310:1400:98064#42 1/2 75b unmapped read.
>>> at net.sf.samtools.BAMIndexer.processAlignment(BAMIndexer.java:94)
>>> at net.sf.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:109)
>>> ... 4 more
>>> Caused by: java.lang.ArrayIndexOutOfBoundsException: 8304
>>> at net.sf.samtools
>>> .BAMIndexer$BAMIndexBuilder.processAlignment(BAMIndexer.java:219)
>>> at net.sf.samtools.BAMIndexer.processAlignment(BAMIndexer.java:92)
>>> ... 5 more
>>>
>>> Previously, we have not reported this problem.
>>>
>>> Thanks. Best regards,
>>>
>>> Antonio M. Agraz
>>>
>>>
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>>
>
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