[Tue Aug 16 04:11:02 CDT 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels-dissimilar-contigs.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null/blah CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:02 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
[Tue Aug 16 04:11:02 CDT 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1747451904
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Tue Aug 16 04:11:02 CDT 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels-bad-samples.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:02 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
[Tue Aug 16 04:11:02 CDT 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1747451904
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Tue Aug 16 04:11:02 CDT 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels-no-contigs.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/dev/null VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=true CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:02 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
[Tue Aug 16 04:11:02 CDT 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1747451904
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Tue Aug 16 04:11:02 CDT 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels.vcf, testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/tmp/merge-indels-snps-test-output.4833367074865223165.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:02 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:11:02 SortVcf Reading entries from input file 1
INFO 2016-08-16 04:11:02 SortVcf Reading entries from input file 2
[Tue Aug 16 04:11:02 CDT 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1747451904
[Tue Aug 16 04:11:02 CDT 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-random-scatter-0.vcf, testdata/picard/vcf/CEUTrio-random-scatter-1.vcf, testdata/picard/vcf/CEUTrio-random-scatter-2.vcf, testdata/picard/vcf/CEUTrio-random-scatter-3.vcf, testdata/picard/vcf/CEUTrio-random-scatter-4.vcf, testdata/picard/vcf/CEUTrio-random-scatter-5.vcf] OUTPUT=/tmp/random-scatter-test-output.8961497088740649479.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:02 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:11:03 SortVcf Reading entries from input file 1
INFO 2016-08-16 04:11:03 SortVcf Reading entries from input file 2
INFO 2016-08-16 04:11:03 SortVcf Reading entries from input file 3
INFO 2016-08-16 04:11:03 SortVcf Reading entries from input file 4
INFO 2016-08-16 04:11:03 SortVcf Reading entries from input file 5
INFO 2016-08-16 04:11:03 SortVcf Reading entries from input file 6
[Tue Aug 16 04:11:03 CDT 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1747451904
[Tue Aug 16 04:11:03 CDT 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-snps.vcf] OUTPUT=/tmp/sort-presorted-test-output.890043062865119995.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:03 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:11:03 SortVcf Reading entries from input file 1
[Tue Aug 16 04:11:03 CDT 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1747451904
[Tue Aug 16 04:11:03 CDT 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels.vcf, testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf] OUTPUT=/tmp/sort-scrambled-indels-snps-test-output.5272763878367470776.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:03 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:11:03 SortVcf Reading entries from input file 1
INFO 2016-08-16 04:11:03 SortVcf Reading entries from input file 2
[Tue Aug 16 04:11:03 CDT 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1747451904
[Tue Aug 16 04:11:03 CDT 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-indels-scrambled.1.vcf, testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf] OUTPUT=/tmp/merge-indels-snps-test-output.2356303915443985888.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:03 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:11:03 SortVcf Reading entries from input file 1
INFO 2016-08-16 04:11:03 SortVcf Reading entries from input file 2
[Tue Aug 16 04:11:03 CDT 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1747451904
[Tue Aug 16 04:11:03 CDT 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf] OUTPUT=/tmp/sort-single-scrambled-test-output.7090712410215760106.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:03 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:11:03 SortVcf Reading entries from input file 1
[Tue Aug 16 04:11:03 CDT 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1747451904
[Tue Aug 16 04:11:03 CDT 2016] picard.vcf.SortVcf INPUT=[testdata/picard/vcf/CEUTrio-snps-scrambled.1.vcf, testdata/picard/vcf/vcfFormatTest.scrambled.vcf] OUTPUT=/tmp/sort-multiple-scrambled-test-output.7959414438762448687.vcf CREATE_INDEX=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:03 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO 2016-08-16 04:11:03 SortVcf Reading entries from input file 1
INFO 2016-08-16 04:11:03 SortVcf Reading entries from input file 2
[Tue Aug 16 04:11:03 CDT 2016] picard.vcf.SortVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1747451904