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picard addorreplacereadgroups output issue

I have a 189GB bam file and I need to add a readgroup in order to do downstream steps, so I used picard AddOrReplaceReadGroups to do it. Below is my command:

java -Xmx8g -jar $PICARD AddOrReplaceReadGroups \  
I=${name}.bam \
O=${name}.addRG.bam \
SORT_ORDER=coordinate \
RGID=${name} \
RGLB=lib1 \
RGPL=illumina \
RGPU=unit1 \
RGSM=${GP}.${name}

However, the output is only 14GB, I think there is sometimes wrong, but it didn't generate any error. Anyone can give me advice on that, thanks.

gatk picard readgroups sequencing java
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written by Peter Chung Peter Chung

Hello Peter Chung ,

is there enough space left on your device? Do you have enough RAM? You could also try samtools addreplacerg: 

$ samtools addreplacerg -r 'ID:${name}' -r 'LB:lib1' -r 'PL:illumina' -r 'PU:unit1' -r 'SM:${GP}.${name}' -o ${name}.addRG.bam ${name}.bam

fin swimmer

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written by finswimmer finswimmer

Changed the label to "QUESTION" from "TOOL". The label TOOL is used to announce new tools to public.

• 1 views • link
written by lakhujanivijay lakhujanivijay

I think there is sometimes wrong, but it didn't generate any error.

what were the last logs on the screen ?

• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

As you may already know, it's also possible (quicker and easier) to add read groups during the alignment step. That's something for your next analysis, then.

• 1 views • link
written by WouterDeCoster WouterDeCoster

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