Java memory requirements for Picard index?

classic Classic list List threaded Threaded
3 messages Options
| Threaded
Open this post in threaded view
|

Java memory requirements for Picard index?

Previti
Dear all,
I seemly have a java issue (out of memory) when trying to construct a picard index for the rat (rn6) genome build using the picard_index_builder_data_manager.
This is strange because other, bigger genomes have not presented any problems...

Does anybody have any suggestions?

Cheers,
Christopher Previti

Fatal error: Exit code 1 ()
[Thu Jul 06 08:26:48 UTC 2017] picard.sam.CreateSequenceDictionary REFERENCE=/opt/galaxy/galaxy/database/jobs_directory/000/978/dataset_1974_files/rn6.fa OUTPUT=rn6.dict    TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=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
[Thu Jul 06 08:26:48 UTC 2017] Executing as [hidden email] on Linux 3.10.0-514.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 2.7.1-SNAPSHOT
[Thu Jul 06 08:26:49 UTC 2017] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1051721728
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
	at htsjdk.samtools.reference.FastaSequenceFile.readSequence(FastaSequenceFile.java:151)
	at htsjdk.samtools.reference.FastaSequenceFile.nextSequence(FastaSequenceFile.java:81)
	at picard.sam.CreateSequenceDictionary.makeSequenceDictionary(CreateSequenceDictionary.java:156)
	at picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:137)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
Error building index.






--
Dr. Christopher Previti
Genomics and
Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4434

christopher.previti@...
www.dkfz.de

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.



    

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
| Threaded
Open this post in threaded view
|

Re: Java memory requirements for Picard index?

Björn Grüning-3
Hi Christopher,

you can increase the JVM memory options via the job_conf.xml file for a
particular tool.

Hope this helps,
Bjoern

Am 06.07.2017 um 13:05 schrieb Previti:

> Dear all,
> I seemly have a java issue (out of memory) when trying to construct a
> picard index for the rat (rn6) genome build using the
> picard_index_builder_data_manager.
> This is strange because other, bigger genomes have not presented any
> problems...
>
> Does anybody have any suggestions?
>
> Cheers,
> Christopher Previti
>
> Fatal error: Exit code 1 ()
> [Thu Jul 06 08:26:48 UTC 2017] picard.sam.CreateSequenceDictionary REFERENCE=/opt/galaxy/galaxy/database/jobs_directory/000/978/dataset_1974_files/rn6.fa OUTPUT=rn6.dict    TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=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
> [Thu Jul 06 08:26:48 UTC 2017] Executing as [hidden email] on Linux 3.10.0-514.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 2.7.1-SNAPSHOT
> [Thu Jul 06 08:26:49 UTC 2017] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.03 minutes.
> Runtime.totalMemory()=1051721728
> To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
> Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
> at htsjdk.samtools.reference.FastaSequenceFile.readSequence(FastaSequenceFile.java:151)
> at htsjdk.samtools.reference.FastaSequenceFile.nextSequence(FastaSequenceFile.java:81)
> at picard.sam.CreateSequenceDictionary.makeSequenceDictionary(CreateSequenceDictionary.java:156)
> at picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:137)
> at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
> at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
> at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
> Error building index.
>
>
>
>
>
>
>
> --
> *Dr. Christopher Previti*
> Genomics and Proteomics Core Facility
> High Throughput Sequencing (W190)
> Bioinformatician
>
> German Cancer Research Center (DKFZ)
> Foundation under Public Law
> Im Neuenheimer Feld 580
> 69120 Heidelberg
> Germany
> Room: B2.102 (INF580/TP3)
> Phone: +49 6221 42-4434
>
> [hidden email] <http://www.dkfz.de/>
> www.dkfz.de <http://www.dkfz.de/>
>
> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
> VAT-ID No.: DE143293537
>
> Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
> Personen bestimmt, an die sie adressiert ist.
> Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
> Informationen enthalten. Sollten Sie nicht
> der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
> Absender und löschen Sie die Mitteilung.
> Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
> untersagt.
>
>
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/
| Threaded
Open this post in threaded view
|

Re: Java memory requirements for Picard index?

Previti

Dear Börn,

Sorry for the late response but thanks!

I'll look into it,

Christopher



On 07/07/2017 06:36 PM, Björn Grüning wrote:
Hi Christopher,

you can increase the JVM memory options via the job_conf.xml file for a
particular tool.

Hope this helps,
Bjoern

Am 06.07.2017 um 13:05 schrieb Previti:
Dear all,
I seemly have a java issue (out of memory) when trying to construct a
picard index for the rat (rn6) genome build using the
picard_index_builder_data_manager.
This is strange because other, bigger genomes have not presented any
problems...

Does anybody have any suggestions?

Cheers,
Christopher Previti

Fatal error: Exit code 1 ()
[Thu Jul 06 08:26:48 UTC 2017] picard.sam.CreateSequenceDictionary REFERENCE=/opt/galaxy/galaxy/database/jobs_directory/000/978/dataset_1974_files/rn6.fa OUTPUT=rn6.dict    TRUNCATE_NAMES_AT_WHITESPACE=true NUM_SEQUENCES=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
[Thu Jul 06 08:26:48 UTC 2017] Executing as [hidden email] on Linux 3.10.0-514.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_92-b15; Picard version: 2.7.1-SNAPSHOT
[Thu Jul 06 08:26:49 UTC 2017] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1051721728
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
	at htsjdk.samtools.reference.FastaSequenceFile.readSequence(FastaSequenceFile.java:151)
	at htsjdk.samtools.reference.FastaSequenceFile.nextSequence(FastaSequenceFile.java:81)
	at picard.sam.CreateSequenceDictionary.makeSequenceDictionary(CreateSequenceDictionary.java:156)
	at picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:137)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
Error building index.







-- 
*Dr. Christopher Previti*
Genomics and Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4434

[hidden email] <http://www.dkfz.de/>
www.dkfz.de <http://www.dkfz.de/>

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die
Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte
Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den
Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist
untersagt.




___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/


--
Dr. Christopher Previti
Genomics and
Proteomics Core Facility
High Throughput Sequencing (W190)
Bioinformatician

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
Room: B2.102 (INF580/TP3)
Phone: +49 6221 42-4434

christopher.previti@...
www.dkfz.de

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist.
Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht
der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung.
Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.



    

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/