[Samtools-help] create md5 file when doing MarkDuplicates using picard

[Guoying Qi <gq...@sa...>]

Hi, there

I added one option for Picard MarkDuplicates command to generate the bam 
md5 file: CREATE_MD5_FILE=TRUE

However, sometimes  it works and sometimes not.

If not working, it will work if I change TRUE to true like this: 
CREATE_MD5_FILE=true.

No matter I use big TRUE or small true, Picard will always print out 
'CREATE_MD5_FILE=true'.

I used the big TRUE in the following example, and no 
5404_1_mk_gq1.bam.md5 file generated.

Can somebody check what I did wrong?

Thank you very much!

Guoying Qi

sf-2-1-01[gq1]16: /software/bin/java -Xmx3000m -jar 
/software/solexa/bin/aligners/picard/current/MarkDuplicates.jar 
INPUT=/nfs/sf12/IL9/analysis/101019_IL9_05404/Data/Intensities/Bustard1.8.1a2_26-10-2010_RTA/GERALD_26-10-2010_RTA/archive/5404_1.bam 
OUTPUT=/nfs/sf12/IL9/analysis/101019_IL9_05404/Data/Intensities/Bustard1.8.1a2_26-10-2010_RTA/GERALD_26-10-2010_RTA/archive/5404_1_mk_gq1.bam 
METRICS_FILE=/tmp/5404_1_gq1 TMP_DIR=/tmp/ 
VALIDATION_STRINGENCY='SILENT' 
MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP='900' REMOVE_DUPLICATES='false' 
ASSUME_SORTED='true' VERBOSITY='ERROR' 
READ_NAME_REGEX='[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*' 
CREATE_MD5_FILE=TRUE
[Wed Oct 27 16:52:20 BST 2010] net.sf.picard.sam.MarkDuplicates 
INPUT=/nfs/sf12/IL9/analysis/101019_IL9_05404/Data/Intensities/Bustard1.8.1a2_26-10-2010_RTA/GERALD_26-10-2010_RTA/archive/5404_1.bam 
OUTPUT=/nfs/sf12/IL9/analysis/101019_IL9_05404/Data/Intensities/Bustard1.8.1a2_26-10-2010_RTA/GERALD_26-10-2010_RTA/archive/5404_1_mk_gq1.bam 
METRICS_FILE=/tmp/5404_1_gq1 REMOVE_DUPLICATES=false ASSUME_SORTED=true 
MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=900 
READ_NAME_REGEX=[a-zA-Z0-9_]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* 
TMP_DIR=/tmp VERBOSITY=ERROR VALIDATION_STRINGENCY=SILENT 
CREATE_MD5_FILE=true    OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 QUIET=false 
COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false
[Wed Oct 27 16:52:30 BST 2010] net.sf.picard.sam.MarkDuplicates done.
Runtime.totalMemory()=961937408
sf-2-1-01[gq1]17: ls *bam* 
 5404_1.bam  5404_1_mk_gq1.bam 


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