Standard error
[Tue Aug 16 04:11:55 CDT 2016] picard.vcf.LiftoverVcf INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/vcf/testLiftover.vcf OUTPUT=/tmp/LiftoverVcfsTest1849640003443624182.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/test.over.chain REJECT=/tmp/LiftoverVcfsTest1849640003443624182.tmp/reject-delete-me.vcf REFERENCE_SEQUENCE=testdata/picard/vcf/dummy.reference.fasta CREATE_INDEX=false WARN_ON_MISSING_CONTIG=false WRITE_ORIGINAL_POSITION=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:55 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 04:11:55 LiftoverVcf Loading up the target reference genome.
INFO 2016-08-16 04:11:55 LiftoverVcf Lifting variants over and sorting.
INFO 2016-08-16 04:11:55 LiftoverVcf Processed 2 variants.
INFO 2016-08-16 04:11:55 LiftoverVcf 2 variants failed to liftover.
INFO 2016-08-16 04:11:55 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over.
INFO 2016-08-16 04:11:55 LiftoverVcf 100.0000% of variants were not successfully lifted over and written to the output.
INFO 2016-08-16 04:11:55 LiftoverVcf Writing out sorted records to final VCF.
[Tue Aug 16 04:11:55 CDT 2016] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1767374848
[Tue Aug 16 04:11:55 CDT 2016] picard.vcf.LiftoverVcf INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/vcf/testLiftoverUsingMissingContig.vcf OUTPUT=/tmp/LiftoverVcfsTest1849640003443624182.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/test.over.badContig.chain REJECT=/tmp/LiftoverVcfsTest1849640003443624182.tmp/reject-delete-me.vcf REFERENCE_SEQUENCE=testdata/picard/vcf/dummy.reference.fasta WARN_ON_MISSING_CONTIG=false CREATE_INDEX=false WRITE_ORIGINAL_POSITION=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:55 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 04:11:55 LiftoverVcf Loading up the target reference genome.
INFO 2016-08-16 04:11:55 LiftoverVcf Lifting variants over and sorting.
ERROR 2016-08-16 04:11:55 LiftoverVcf Encountered a contig, missingContig that is not part of the target reference.
[Tue Aug 16 04:11:55 CDT 2016] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1767374848
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Tue Aug 16 04:11:55 CDT 2016] picard.vcf.LiftoverVcf INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/vcf/testLiftoverUsingMissingContig.vcf OUTPUT=/tmp/LiftoverVcfsTest1849640003443624182.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/test.over.badContig.chain REJECT=/tmp/LiftoverVcfsTest1849640003443624182.tmp/reject-delete-me.vcf REFERENCE_SEQUENCE=testdata/picard/vcf/dummy.reference.fasta WARN_ON_MISSING_CONTIG=true CREATE_INDEX=false WRITE_ORIGINAL_POSITION=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:55 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 04:11:55 LiftoverVcf Loading up the target reference genome.
INFO 2016-08-16 04:11:55 LiftoverVcf Lifting variants over and sorting.
WARNING 2016-08-16 04:11:55 LiftoverVcf Encountered a contig, missingContig that is not part of the target reference.
INFO 2016-08-16 04:11:55 LiftoverVcf Processed 2 variants.
INFO 2016-08-16 04:11:55 LiftoverVcf 2 variants failed to liftover.
INFO 2016-08-16 04:11:55 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over.
INFO 2016-08-16 04:11:55 LiftoverVcf 100.0000% of variants were not successfully lifted over and written to the output.
INFO 2016-08-16 04:11:55 LiftoverVcf Writing out sorted records to final VCF.
[Tue Aug 16 04:11:55 CDT 2016] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1767374848
[Tue Aug 16 04:11:55 CDT 2016] picard.vcf.LiftoverVcf INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/vcf/testLiftover.vcf OUTPUT=/tmp/LiftoverVcfsTest1849640003443624182.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/test.over.chain REJECT=/tmp/LiftoverVcfsTest1849640003443624182.tmp/reject-delete-me.vcf REFERENCE_SEQUENCE=testdata/picard/vcf/dummy.reference.fasta WRITE_ORIGINAL_POSITION=false CREATE_INDEX=false WARN_ON_MISSING_CONTIG=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:55 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 04:11:55 LiftoverVcf Loading up the target reference genome.
INFO 2016-08-16 04:11:55 LiftoverVcf Lifting variants over and sorting.
INFO 2016-08-16 04:11:55 LiftoverVcf Processed 2 variants.
INFO 2016-08-16 04:11:55 LiftoverVcf 2 variants failed to liftover.
INFO 2016-08-16 04:11:55 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over.
INFO 2016-08-16 04:11:55 LiftoverVcf 100.0000% of variants were not successfully lifted over and written to the output.
INFO 2016-08-16 04:11:55 LiftoverVcf Writing out sorted records to final VCF.
[Tue Aug 16 04:11:55 CDT 2016] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1767374848
[Tue Aug 16 04:11:55 CDT 2016] picard.vcf.LiftoverVcf INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/vcf/testLiftover.vcf OUTPUT=/tmp/LiftoverVcfsTest1849640003443624182.tmp/lift-delete-me.vcf CHAIN=testdata/picard/vcf/test.over.chain REJECT=/tmp/LiftoverVcfsTest1849640003443624182.tmp/reject-delete-me.vcf REFERENCE_SEQUENCE=testdata/picard/vcf/dummy.reference.fasta WRITE_ORIGINAL_POSITION=true CREATE_INDEX=false WARN_ON_MISSING_CONTIG=false LIFTOVER_MIN_MATCH=1.0 ALLOW_MISSING_FIELDS_IN_HEADER=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:55 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 04:11:55 LiftoverVcf Loading up the target reference genome.
INFO 2016-08-16 04:11:55 LiftoverVcf Lifting variants over and sorting.
INFO 2016-08-16 04:11:55 LiftoverVcf Processed 2 variants.
INFO 2016-08-16 04:11:55 LiftoverVcf 2 variants failed to liftover.
INFO 2016-08-16 04:11:55 LiftoverVcf 0 variants lifted over but had mismatching reference alleles after lift over.
INFO 2016-08-16 04:11:55 LiftoverVcf 100.0000% of variants were not successfully lifted over and written to the output.
INFO 2016-08-16 04:11:55 LiftoverVcf Writing out sorted records to final VCF.
[Tue Aug 16 04:11:55 CDT 2016] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664