picard metrics error

[krapulaxdoctor]

Dear all,
I would like to ask for help to solve this issue with Picard tools:

I already looked through forums, picard FAQ, but I id not find similar problems.

I would like to run the CollectOxoGMetrics command to test my datafiles.
For this i used the following command:

user@work:~$ java -jar -Xmx6g /picard/dist/picard.jar CollectOxoGMetrics R=/mm10-Genome/genome.fa I=rnaseq.bam O=picard-oxo-output.txt

the program starts up and writes some line:

[Fri Oct 23 13:15:24 CEST 2015] picard.analysis.CollectOxoGMetrics INPUT=rnaseq.bam OUTPUT=picard-oxo-output.txt REFERENCE_SEQUENCE=/mm10-Genome/genome.fa MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 USE_OQ=true CONTEXT_SIZE=1 STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Fri Oct 23 13:15:24 CEST 2015] Executing as user@work on Linux 3.13.0-65-generic amd64; OpenJDK 64-Bit Server VM 1.7.0_79-b14; Picard version: 1.135(a61ab80f95b753621cb252b17f2234d8bcb77096_1436675286) JdkDeflater
INFO 2015-10-23 13:15:24 CollectOxoGMetrics Generated 16 context strings.
INFO 2015-10-23 13:15:24 CollectOxoGMetrics Loading dbSNP File: null
INFO 2015-10-23 13:15:24 CollectOxoGMetrics Starting iteration.

, but after 2 minutes it stops, writing:

[Fri Oct 23 13:17:57 CEST 2015] picard.analysis.CollectOxoGMetrics done. Elapsed time: 2.54 minutes.
Runtime.totalMemory()=229638144

And the text file it generates as output contains a few line:

## htsjdk.samtools.metrics.StringHeader
# picard.analysis.CollectOxoGMetrics INPUT=rnaseq.bam OUTPUT=picard-oxo-output.txt REFERENCE_SEQUENCE=/mm10-Genome/genome.fa MINIMUM_QUALITY_SCORE=20 MINIMUM_MAPPING_QUALITY=30 MINIMUM_INSERT_SIZE=60 MAXIMUM_INSERT_SIZE=600 USE_OQ=true CONTEXT_SIZE=1 STOP_AFTER=2147483647 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Oct 23 13:15:24 CEST 2015

And nothing else.

Then , i wanted to test whether my bam file has a problem, for this i ran

java -jar -Xmx6g /picard/dist/picard.jar ValidateSamFile I=rnaseq.bam O=picard-validate-output.txt

the output files has error messages, (100 lines from which only one is different) such as:

ERROR: Read groups is empty
WARNING: Read name BIOMICS-HISEQLN:157:HMLNVADXX:2:1205:5080:8933, A record is missing a read group
WARNING: Read name BIOMICS-HISEQHI:555:HMLGGADXX:2:1211:16446:43292, A record is missing a read group
WARNING: Read name BIOMICS-HISEQLN:159:HMJFYADXX:1:1205:18060:52304, A record is missing a read group
WARNING: Read name BIOMICS-HISEQHI:555:HMLGGADXX:2:2210:16735:34742, A record is missing a read group
WARNING: Read name BIOMICS-HISEQLN:157:HMLNVADXX:2:1111:19948:49163, A record is missing a read group
WARNING: Read name BIOMICS-HISEQHI:555:HMLGGADXX:2:1111:9860:29396, A record is missing a read group
WARNING: Read name BIOMICS-HISEQLN:157:HMLNVADXX:1:1103:12058:44655, A record is missing a read group
WARNING: Read name BIOMICS-HISEQLN:159:HMJFYADXX:1:2115:4058:6432, A record is missing a read group
WARNING: Read name BIOMICS-HISEQLN:157:HMLNVADXX:1:2208:5115:74838, A record is missing a read group

Could you please suggest me an idea how to deal with this error?
Does picard need more than 8GB memory in general?

Thank you very much for your help. And for your time.


Regards,