picard addorreplacereadgroups output issue

Question

[Peter Chung]

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.

[finswimmer]

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

[lakhujanivijay]

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

[Pierre Lindenbaum]

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

what were the last logs on the screen ?

[WouterDeCoster]

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.