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stderr:
[Thu Apr 30 12:27:00 EDT 2015] Executing as goldba06@interactive5 on Linux 2.6.32-358.23.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_03-b04; Picard version: 1.112(1930) IntelDeflater
[Thu Apr 30 12:27:00 EDT 2015] net.sf.picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1009909760
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" java.lang.NullPointerException
at net.sf.picard.sam.ValidateSamFile.doWork(ValidateSamFile.java:148)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:179)
at net.sf.picard.sam.ValidateSamFile.main(ValidateSamFile.java:101)
@artgoldberg We have a new policy for Picard tools support. For initial questions and bug reports, we ask that you please post in the GATK forum. If we find that there is an actual bug that requires code changes we'll open a github issue ourselves. This helps us manage support to the community.
When you post this to the GATK forum, please clarify whether the issue still happens if you don't specify the MAX_OUTPUT argument. Thanks!
stderr:
[Thu Apr 30 12:27:00 EDT 2015] Executing as goldba06@interactive5 on Linux 2.6.32-358.23.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_03-b04; Picard version: 1.112(1930) IntelDeflater
[Thu Apr 30 12:27:00 EDT 2015] net.sf.picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1009909760
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" java.lang.NullPointerException
at net.sf.picard.sam.ValidateSamFile.doWork(ValidateSamFile.java:148)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:179)
at net.sf.picard.sam.ValidateSamFile.main(ValidateSamFile.java:101)
Although it's documented in http://broadinstitute.github.io/picard/command-line-overview.html
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