This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
Why does Baserecalibrator stop with no error?
First time at 51% through. Same command used got to 32.7%. Then 60.1%.
When I return to computer I havce been kicked out to my $ and no error is displayed.
First time at 51% through. Same command used got to 32.7%. Then 60.1%.....
What may cause this seemingly random eject?
java -Xmx8g -jar /usr/local/bin/GenomeAnalysisTK-2.3-9-ge5ebf34/GenomeAnalysisTK.jar -T BaseRecalibrator -R human.fa -I OD37.marked.realigned.fixed.bam -knownSites dbsnp_137.b37.vcf -knownSites Mills_and_1000G_gold_standard.indels.b37.sites.vcf -knownSites ALL.wgs.phase1_release_v2.20101123.snps_indels_sv.sites.vcf -o OD37_recal.grp -plots OD37_recal.grp.pdf