Class picard.sam.CompareSAMsTest

all > picard.sam > CompareSAMsTest
14

tests
0

failures
0

ignored
0.057s

duration
100%

successful

Tests

Test Duration Result
testBiggerSequenceDictionaries 0.007s passed
testGroupWithSameCoordinate 0.004s passed
testGroupWithSameCoordinateAndNoMatchInOther 0.004s passed
testGroupWithSameCoordinateSamePosition 0.004s passed
testHasNonPrimary 0.005s passed
testIdentical 0.003s passed
testMoreOnOneSide 0.005s passed
testSequenceDictionariesDifferent1 0.004s passed
testSequenceDictionariesDifferent2 0.003s passed
testSortsDifferent 0.003s passed
testUnmapped1 0.004s passed
testUnmapped2 0.004s passed
testUnmapped3 0.003s passed
testUnmapped4 0.004s passed

Standard output

Match	2
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files match.
Match	2
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files match.
Match	3
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	1
Missing_right	2
SAM files differ.
Match	3
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	2
Missing_right	1
SAM files differ.
Match	0
Differ	5
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files differ.
Match	0
Differ	5
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files differ.
Match	2
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files match.
Match	2
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files match.
Match	2
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files match.
Match	2
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files match.
Match	2
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files match.
Match	2
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files match.
Match	3
Differ	2
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	3
Missing_right	0
SAM files differ.
Match	3
Differ	2
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	3
SAM files differ.
Name of sequence record 1 differs.
/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam: chr20
/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/chr21.sam: chr21
Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
Match	0
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files differ.
Name of sequence record 1 differs.
/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/chr21.sam: chr21
/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam: chr20
Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
Match	0
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files differ.
Length of sequence dictionaries differs.
/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam: 1
/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam: 2
Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
Match	0
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files differ.
Length of sequence dictionaries differs.
/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam: 2
/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam: 1
Cannot compare coordinate-sorted SAM files because sequence dictionaries differ.
Match	0
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files differ.
Sort order differs.
/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam: coordinate
/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unsorted.sam: null
Sort Order differs.
/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam: coordinate
/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unsorted.sam: unsorted
Cannot compare alignments if sort orders differ.
Match	0
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files differ.
Sort order differs.
/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unsorted.sam: null
/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam: coordinate
Sort Order differs.
/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unsorted.sam: unsorted
/bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam: coordinate
Cannot compare alignments if sort orders differ.
Match	0
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files differ.
Match	1
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	1
Missing_left	0
Missing_right	0
SAM files differ.
Match	1
Differ	0
Unmapped_both	0
Unmapped_left	1
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files differ.
Match	1
Differ	0
Unmapped_both	0
Unmapped_left	0
Unmapped_right	1
Missing_left	0
Missing_right	0
SAM files differ.
Match	1
Differ	0
Unmapped_both	0
Unmapped_left	1
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files differ.
Match	0
Differ	0
Unmapped_both	0
Unmapped_left	1
Unmapped_right	1
Missing_left	0
Missing_right	0
SAM files differ.
Match	0
Differ	0
Unmapped_both	0
Unmapped_left	1
Unmapped_right	1
Missing_left	0
Missing_right	0
SAM files differ.
Match	1
Differ	0
Unmapped_both	1
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files match.
Match	1
Differ	0
Unmapped_both	1
Unmapped_left	0
Unmapped_right	0
Missing_left	0
Missing_right	0
SAM files match.

Standard error

[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/group_same_coord.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/group_same_coord_diff_order.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/group_same_coord_diff_order.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/group_same_coord.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/group_same_coord.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/diff_coords.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/diff_coords.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/group_same_coord.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_same_position.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/has_non_primary.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/has_non_primary.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_5.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_5_plus.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted_5.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/chr21.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/chr21.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/bigger_seq_dict.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unsorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unsorted.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unmapped_second.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unmapped_second.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/genomic_sorted.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unmapped_second.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unmapped_second.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.CompareSAMs /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam /bar/jli/Chip-seq/script/picard/testdata/picard/sam/CompareSAMs/unmapped_first.sam    VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:37 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 04:11:37 CDT 2016] picard.sam.CompareSAMs done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952