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Preparation for point release of read calibrator: no artificial heap size limit, no duplicate dbsnp records. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@986 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-06-11 18:39:33 +00:00
parent 63b5c12cbd
commit 5440dd13df
2 changed files with 12 additions and 1 deletions
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11
doc/ReadQualityRecalibrator/README
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@ -97,6 +97,17 @@ Known Issues
graphs. If running on a machine via ssh, be certain graphs. If running on a machine via ssh, be certain
to enable X tunnelling. to enable X tunnelling.
Troubleshooting
---------------
- The memory requirements of the recalibrator will
vary based on the type of JVM running the application
and the number of read groups in the input bam file.
If the application reports 'java.lang.OutOfMemoryError:
Java heap space', increase the max heap size provided
to the JVM by adding ' -Xmx????m' to the jvm_args
variable in RecalQual.py, where '????' is the maximum
available memory on the processing computer.
Support Support
------- -------
For support, please email gsadevelopers@broad.mit.edu. For support, please email gsadevelopers@broad.mit.edu.

2
python/RecalQual.py
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@ -6,7 +6,7 @@ java_exe='/broad/tools/Linux/x86_64/pkgs/jdk_1.6.0_12/bin/java'
R_exe="/broad/tools/apps/R-2.6.0/bin/Rscript" R_exe="/broad/tools/apps/R-2.6.0/bin/Rscript"
# Any special site-specific arguments to pass the JVM. # Any special site-specific arguments to pass the JVM.
jvm_args='-ea -Xmx4096m' jvm_args='-ea'
# Which platforms should the calibration tool be run over? # Which platforms should the calibration tool be run over?
platforms=['illumina'] platforms=['illumina']