We use Picard/CleanSama.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, to mark duplicates:
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.
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, to mark duplicates:
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.
