I am trying to remove PCR duplicates using Picard.
My header looks like this:
But I get this error when I run Picard.
Samtools can read it ok and it tells me :
Why can't Picard Read it?
My header looks like this:
Code:
@HD VN:1.0 SO:sorted @PG ID:TopHat VN:1.0.14 CL:/home/guo/bin/tophat -G ../../hg19.GFF3 -g 1 -o Dex -r 160 --solexa1.3-quals -p 4 ../../../../bowtie-0.12.3/indexes/hg19 ../../FASTQ/KUMC_PE_RNASEQ_sample6_1_sequence.txt ../../FASTQ/KUMC_PE_RNASEQ_sample6_2_sequence.txt @SQ SN:chr1 LN:249250621 @SQ SN:chr2 LN:243199373 @SQ SN:chr3 LN:198022430 @SQ SN:chr4 LN:191154276 @SQ SN:chr5 LN:180915260 @SQ SN:chr6 LN:171115067 @SQ SN:chr7 LN:159138663 @SQ SN:chr8 LN:146364022 @SQ SN:chr9 LN:141213431 @SQ SN:chr10 LN:135534747 @SQ SN:chr11 LN:135006516 @SQ SN:chr12 LN:133851895 @SQ SN:chr13 LN:115169878 @SQ SN:chr14 LN:107349540 @SQ SN:chr15 LN:102531392 @SQ SN:chr16 LN:90354753 @SQ SN:chr17 LN:81195210 @SQ SN:chr18 LN:78077248 @SQ SN:chr19 LN:59128983 @SQ SN:chr20 LN:63025520 @SQ SN:chr21 LN:48129895 @SQ SN:chr22 LN:51304566 @SQ SN:chrX LN:155270560 @SQ SN:chrY LN:59373566 @SQ SN:chrM LN:16571
Code:
net.sf.picard.sam.MarkDuplicates INPUT=Dex.bam OUTPUT=Dex.NoDup.bam METRICS_FILE=Dex.Metrics REMOVE_DUPLICATES=true 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 TMP_DIR=/tmp/shart3 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false INFO 2010-08-19 12:25:28 MarkDuplicates Start of doWork freeMemory: 31023560; totalMemory: 31588352; maxMemory: 620756992 INFO 2010-08-19 12:25:28 MarkDuplicates Reading input file and constructing read end information. INFO 2010-08-19 12:25:28 MarkDuplicates Will retain up to 2463321 data points before spilling to disk. [Thu Aug 19 12:25:28 CDT 2010] net.sf.picard.sam.MarkDuplicates done. Runtime.totalMemory()=51314688 Exception in thread "main" java.lang.IllegalArgumentException: No enum const class net.sf.samtools.SAMFileHeader$SortOrder.sorted
Code:
46021417 in total 0 QC failure 0 duplicates 46021417 mapped (100.00%) 46021417 paired in sequencing 23145972 read1 22875445 read2 33385558 properly paired (72.54%) 39196142 with itself and mate mapped 6825275 singletons (14.83%) 0 with mate mapped to a different chr 0 with mate mapped to a different chr (mapQ>=5)
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