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lpantano / mirdeep2_core

Main core scripts for novel mirna discovery from bam files
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Qualimap allows to set RAM size using special argument: --java-mem-size #5

Open ro6ert opened 5 years ago

ro6ert commented 5 years ago

Hello Lorena,

Is there an option to give Qualimap more memory?

Best, -Rob

Mon Nov 26 15:36:16 EST 2018 WARNING Output folder already exists, the results will be saved there Initializing regions from /proj/sadevs/sadev00/exome_pipeline/bcbio/genomes/Hsapiens/hg19/rnaseq/ref-transcripts.gtf... Initialized 100000 regions... Initialized 200000 regions... Initialized 300000 regions... Initialized 400000 regions... Initialized 500000 regions... Initialized 600000 regions... Initialized 700000 regions... Initialized 800000 regions... Initialized 900000 regions... Initialized 1000000 regions... Initialized 1100000 regions... Initialized 1200000 regions... Initialized 1300000 regions... Initialized 1400000 regions... Initialized 1500000 regions... Initialized 1600000 regions... Initialized 1700000 regions... WARNING: out of memory! Qualimap allows to set RAM size using special argument: --java-mem-size Check more details using --help command or read the manual. ' returned non-zero exit status 1

lpantano commented 5 years ago

Hi,

you can use the resource section in the yaml file: https://bcbio-nextgen.readthedocs.io/en/latest/contents/configuration.html#resources

something like this:

resources:
  qualimap:
     memory: 6G

Cheers

On Mon, Nov 26, 2018 at 4:59 PM ro6ert notifications@github.com wrote:

Hello Lorena,

Is there an option to give Qualimap more memory?

Best, -Rob

Mon Nov 26 15:36:16 EST 2018 WARNING Output folder already exists, the results will be saved there Initializing regions from /proj/sadevs/sadev00/exome_pipeline/bcbio/genomes/Hsapiens/hg19/rnaseq/ref-transcripts.gtf... Initialized 100000 regions... Initialized 200000 regions... Initialized 300000 regions... Initialized 400000 regions... Initialized 500000 regions... Initialized 600000 regions... Initialized 700000 regions... Initialized 800000 regions... Initialized 900000 regions... Initialized 1000000 regions... Initialized 1100000 regions... Initialized 1200000 regions... Initialized 1300000 regions... Initialized 1400000 regions... Initialized 1500000 regions... Initialized 1600000 regions... Initialized 1700000 regions... WARNING: out of memory! Qualimap allows to set RAM size using special argument: --java-mem-size Check more details using --help command or read the manual. ' returned non-zero exit status 1

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