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  • I have posted the bug report with filename splitsam_3_3_error.tgz Please let me know if you have further questions.
  • Yeah, I can confirm /opt/java/jdk1.7.0_25/bin/java -Xms256m -Xmx10g -XX:-UseGCOverheadLimit -Djava.io.tmpdir=/scratch/gabow/ -jar /opt/common/gatk/GenomeAnalysisTK-3.2-0-g289df4b/GenomeAnalysisTK.jar -T SplitSamFile -R /ifs/data/bio/assemblies/H.sap…
  • We don't seem to see significant speed up when running with -pairHMM VECTOR_LOGLESS_CACHING on HaplotypeCaller. We seem to meet the requirements (Xeon CPU E5-2670, AVX, Linux 2.6.32), but the performance actually decreased (89 minutes without the pa…
  • Yeah, I get that, but I am just wondering if Queue attempts to balance the size of scattered elements at all. Like in my example, chrDecoy is significantly bigger than chrUn_gl000244, chrUn_gl000245, etc. so it would make a bit more sense to see tem…
  • I'm a bit confused. There was a fix to the above problem in the nightly build but it doesn't look like it's made it into the 2.6-5. The release notes say there were bug fixes in ReduceReads, so I was guessing this fix would be in there. However, the…
  • Hi, I think the link at the bottom "Queue with Grid Engine" should point to: http://www.broadinstitute.org/gatk/guide/article?id=1313 and I think the QFunction link and Command Line options should both now point to: broadinstitute.org/gatk…
  • The new version works like a charm. Thanks.
  • I uploaded the file as ReduceRead_adouble2_chr4_2702605-2702630.bam at the root level of your ftp site. And I realize that you were making a joke above, but I do feel bad that I wasn't able to pinpoint it further than an off-by-one error. It's not t…
  • For what it's worth, I was able to duplicate this error in a small bam (10 reads, region of 25 bases). Stepping through things in a debugger, it looks like there may be an off by one error in SlidingWindow at line 890, as my debugger showed: this.ma…
  • I have been getting this error too. The bam is validated, and reduced reads walked runs fine if the bam is split out into two by sample and run on each individual file. I tried the official 2.6 release and several of the nightly builds and still got…