Help! Picard`s AddOrReplaceReadGroups.jar t

[gogooma]

To whom it may concern,

I want to work with SNP calling using GATK.

I`ve been trying to use the Picard`s AddOrReplaceReadGroups.jar tool to convert sam file to bam file.
But Picard stopped(without any error message). This size of sam file is 40Gb and I think this is bigger than my computer memory.

My file size is 30Gb fastq file.

My work flow is follow:

1) bwa index -a bwtsw hg19

2) bwa aln -t 6 hg19 sample.fastq > sample.sai

3) bwa samse hg19 sample.sai sample.fastq > sample.sam --> 40Gb

4) java -Djava.io.tmpdir=/tmp -Xmx8g -jar /myPath/AddOrReplaceReadGroups.jar \
INPUT=sample.sam OUTPUT=sample.addRG.bam \
SORT_ORDER=coordinate \
RGID=sample RGLB=sampleLIB RGPL=ILLUMINA \
RGPU=NONE RGSM=sample \
VALIDATION_STRINGENCY=LENIENT

---------------------------------------------------------------------------------------
Problem happens when I run step 4. Whenever I run this step, the process stop and I am not able to do anything.

I would appreciate any help.

[spartan29]

what is the actual error message? Plz post that. There should be some error message visible on the terminal..

[gogooma]

--------------------process Message-----------------------------------------
INFO AddOrReplaceReadGroups Processed 1,000,000 ...
INFO AddOrReplaceReadGroups Processed 2,000,000 ...
:
:
INFO AddOrReplaceReadGroups Processed 196,000,000
---------------------------------------------------------------------------------

There is not any message. I think that hang on. I wait for long time but noting happened.

[wzhangvv]

try add this parameter -XX:PermSize=8g -XX:MaxPermSize=8g after -Xmx8g. It will assign more java heap space to picards

To whom it may concern,

I want to work with SNP calling using GATK.

I`ve been trying to use the Picard`s AddOrReplaceReadGroups.jar tool to convert sam file to bam file.
But Picard stopped(without any error message). This size of sam file is 40Gb and I think this is bigger than my computer memory.

My file size is 30Gb fastq file.

My work flow is follow:

1) bwa index -a bwtsw hg19

2) bwa aln -t 6 hg19 sample.fastq > sample.sai

3) bwa samse hg19 sample.sai sample.fastq > sample.sam --> 40Gb

4) java -Djava.io.tmpdir=/tmp -Xmx8g -jar /myPath/AddOrReplaceReadGroups.jar \
INPUT=sample.sam OUTPUT=sample.addRG.bam \
SORT_ORDER=coordinate \
RGID=sample RGLB=sampleLIB RGPL=ILLUMINA \
RGPU=NONE RGSM=sample \
VALIDATION_STRINGENCY=LENIENT

---------------------------------------------------------------------------------------
Problem happens when I run step 4. Whenever I run this step, the process stop and I am not able to do anything.

I would appreciate any help.