I ran the following command
java -Xmx130g -Xms80g -Djava.io.tmpdir=javatmp/ -jar ~/picard.jar CollectHsMetrics BAIT_INTERVALS=annotations/NexteraRapidCapture_Exome_Probes_v1.2.interval_list TARGET_INTERVALS=annotations/nexterarapidcapture_exome_targetedregions_v1.2.no_chr.MT.interval_list INPUT=sample.bam OUTPUT=sample.hsmetrics METRIC_ACCUMULATION_LEVEL=ALL_READS QUIET=true VALIDATION_STRINGENCY=SILENT 2> sample.hsmetrics.log
and the program seems got stuck at a certain step. The last line in the log file is
INFO 2017-03-30 10:15:28 TheoreticalSensitivity Calculating theoretical het sensitivity
The input bam file is from gatk LeftAlignIndels. The above command worked fine on other input files generated the same way. I also tried CalculateHsMetrics and got the same problem. I tried picard version 2.3.0 and the latest 2.9.0 with the same problem. It didn't create the expected output file and program kept running (not being idle but consuming cpu time). I'm wondering if the program could enter a endless loop in some special cases. I'd tried leaving the program running for days with no result or error messages (had to kill the program at the end).