Class picard.sam.markduplicates.AsIsMarkDuplicatesTester
Tests
| Test |
Duration |
Result |
| testSameUnclipped5PrimeOppositeStrand[0](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv1.sam) |
1.068s |
passed |
| testSameUnclipped5PrimeOppositeStrand[1](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndv2.sam) |
0.819s |
passed |
| testSameUnclipped5PrimeOppositeStrand[2](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv1.sam) |
0.807s |
passed |
| testSameUnclipped5PrimeOppositeStrand[3](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv2.sam) |
0.804s |
passed |
| testSameUnclipped5PrimeOppositeStrand[4](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv3.sam) |
0.790s |
passed |
| testSameUnclipped5PrimeOppositeStrand[5](testdata/picard/sam/MarkDuplicates/sameUnclipped5primeEndCoordinateSortedv4.sam) |
1.119s |
passed |
Standard error
[Tue Aug 16 04:11:06 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.7493569446250066184.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.7493569446250066184.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.7493569446250066184.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 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 04:11:06 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 04:11:06 MarkDuplicates Start of doWork freeMemory: 1765683960; totalMemory: 1797783552; maxMemory: 1908932608
INFO 2016-08-16 04:11:06 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-08-16 04:11:06 MarkDuplicates Will retain up to 7342048 data points before spilling to disk.
INFO 2016-08-16 04:11:06 MarkDuplicates Read 4 records. 0 pairs never matched.
INFO 2016-08-16 04:11:06 MarkDuplicates After buildSortedReadEndLists freeMemory: 1705015504; totalMemory: 1795162112; maxMemory: 1908932608
INFO 2016-08-16 04:11:06 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk.
INFO 2016-08-16 04:11:06 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2016-08-16 04:11:06 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2016-08-16 04:11:06 MarkDuplicates Sorting list of duplicate records.
INFO 2016-08-16 04:11:06 MarkDuplicates After generateDuplicateIndexes freeMemory: 1258239720; totalMemory: 1769472000; maxMemory: 1908932608
INFO 2016-08-16 04:11:06 MarkDuplicates Marking 1 records as duplicates.
INFO 2016-08-16 04:11:06 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2016-08-16 04:11:06 MarkDuplicates Reads are assumed to be ordered by: queryname
INFO 2016-08-16 04:11:07 MarkDuplicates Before output close freeMemory: 1758243016; totalMemory: 1792540672; maxMemory: 1908932608
INFO 2016-08-16 04:11:07 MarkDuplicates After output close freeMemory: 1735472736; totalMemory: 1769472000; maxMemory: 1908932608
[Tue Aug 16 04:11:07 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1769472000
[Tue Aug 16 04:11:07 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.1363923835886276910.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.1363923835886276910.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.1363923835886276910.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 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 04:11:07 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 04:11:07 MarkDuplicates Start of doWork freeMemory: 1755950432; totalMemory: 1789919232; maxMemory: 1908932608
INFO 2016-08-16 04:11:07 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-08-16 04:11:07 MarkDuplicates Will retain up to 7342048 data points before spilling to disk.
INFO 2016-08-16 04:11:07 MarkDuplicates Read 4 records. 0 pairs never matched.
INFO 2016-08-16 04:11:07 MarkDuplicates After buildSortedReadEndLists freeMemory: 1676734264; totalMemory: 1769472000; maxMemory: 1908932608
INFO 2016-08-16 04:11:07 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk.
INFO 2016-08-16 04:11:07 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2016-08-16 04:11:07 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2016-08-16 04:11:07 MarkDuplicates Sorting list of duplicate records.
INFO 2016-08-16 04:11:07 MarkDuplicates After generateDuplicateIndexes freeMemory: 1275453472; totalMemory: 1788346368; maxMemory: 1908932608
INFO 2016-08-16 04:11:07 MarkDuplicates Marking 1 records as duplicates.
INFO 2016-08-16 04:11:07 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2016-08-16 04:11:07 MarkDuplicates Reads are assumed to be ordered by: queryname
INFO 2016-08-16 04:11:07 MarkDuplicates Before output close freeMemory: 1733513632; totalMemory: 1769472000; maxMemory: 1908932608
INFO 2016-08-16 04:11:07 MarkDuplicates After output close freeMemory: 1750062552; totalMemory: 1785724928; maxMemory: 1908932608
[Tue Aug 16 04:11:07 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1785724928
[Tue Aug 16 04:11:07 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.8835973730304499078.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.8835973730304499078.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.8835973730304499078.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 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 04:11:07 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 04:11:07 MarkDuplicates Start of doWork freeMemory: 1733842880; totalMemory: 1769472000; maxMemory: 1908932608
INFO 2016-08-16 04:11:07 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-08-16 04:11:07 MarkDuplicates Will retain up to 7342048 data points before spilling to disk.
INFO 2016-08-16 04:11:08 MarkDuplicates Read 4 records. 0 pairs never matched.
INFO 2016-08-16 04:11:08 MarkDuplicates After buildSortedReadEndLists freeMemory: 1689230072; totalMemory: 1783627776; maxMemory: 1908932608
INFO 2016-08-16 04:11:08 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk.
INFO 2016-08-16 04:11:08 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2016-08-16 04:11:08 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2016-08-16 04:11:08 MarkDuplicates Sorting list of duplicate records.
INFO 2016-08-16 04:11:08 MarkDuplicates After generateDuplicateIndexes freeMemory: 1255514936; totalMemory: 1769472000; maxMemory: 1908932608
INFO 2016-08-16 04:11:08 MarkDuplicates Marking 2 records as duplicates.
INFO 2016-08-16 04:11:08 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2016-08-16 04:11:08 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2016-08-16 04:11:08 MarkDuplicates Before output close freeMemory: 1744508248; totalMemory: 1781530624; maxMemory: 1908932608
INFO 2016-08-16 04:11:08 MarkDuplicates After output close freeMemory: 1732747952; totalMemory: 1769472000; maxMemory: 1908932608
[Tue Aug 16 04:11:08 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1769472000
[Tue Aug 16 04:11:08 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.7883755260428114985.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.7883755260428114985.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.7883755260428114985.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 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 04:11:08 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 04:11:08 MarkDuplicates Start of doWork freeMemory: 1743788504; totalMemory: 1780482048; maxMemory: 1908932608
INFO 2016-08-16 04:11:08 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-08-16 04:11:08 MarkDuplicates Will retain up to 7342048 data points before spilling to disk.
INFO 2016-08-16 04:11:08 MarkDuplicates Read 4 records. 0 pairs never matched.
INFO 2016-08-16 04:11:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 1674007480; totalMemory: 1769472000; maxMemory: 1908932608
INFO 2016-08-16 04:11:09 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk.
INFO 2016-08-16 04:11:09 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2016-08-16 04:11:09 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2016-08-16 04:11:09 MarkDuplicates Sorting list of duplicate records.
INFO 2016-08-16 04:11:09 MarkDuplicates After generateDuplicateIndexes freeMemory: 1264269616; totalMemory: 1778909184; maxMemory: 1908932608
INFO 2016-08-16 04:11:09 MarkDuplicates Marking 2 records as duplicates.
INFO 2016-08-16 04:11:09 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2016-08-16 04:11:09 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2016-08-16 04:11:09 MarkDuplicates Before output close freeMemory: 1732291408; totalMemory: 1769996288; maxMemory: 1908932608
INFO 2016-08-16 04:11:09 MarkDuplicates After output close freeMemory: 1739929368; totalMemory: 1777336320; maxMemory: 1908932608
[Tue Aug 16 04:11:09 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1777336320
[Tue Aug 16 04:11:09 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.5513872354652556558.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.5513872354652556558.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.5513872354652556558.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 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 04:11:09 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 04:11:09 MarkDuplicates Start of doWork freeMemory: 1732095960; totalMemory: 1769472000; maxMemory: 1908932608
INFO 2016-08-16 04:11:09 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-08-16 04:11:09 MarkDuplicates Will retain up to 7342048 data points before spilling to disk.
INFO 2016-08-16 04:11:09 MarkDuplicates Read 4 records. 0 pairs never matched.
INFO 2016-08-16 04:11:09 MarkDuplicates After buildSortedReadEndLists freeMemory: 1680142824; totalMemory: 1776287744; maxMemory: 1908932608
INFO 2016-08-16 04:11:09 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk.
INFO 2016-08-16 04:11:09 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2016-08-16 04:11:09 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2016-08-16 04:11:09 MarkDuplicates Sorting list of duplicate records.
INFO 2016-08-16 04:11:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 1254394064; totalMemory: 1769472000; maxMemory: 1908932608
INFO 2016-08-16 04:11:10 MarkDuplicates Marking 2 records as duplicates.
INFO 2016-08-16 04:11:10 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2016-08-16 04:11:10 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2016-08-16 04:11:10 MarkDuplicates Before output close freeMemory: 1737096520; totalMemory: 1775239168; maxMemory: 1908932608
INFO 2016-08-16 04:11:10 MarkDuplicates After output close freeMemory: 1731627704; totalMemory: 1769472000; maxMemory: 1908932608
[Tue Aug 16 04:11:10 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1769472000
[Tue Aug 16 04:11:10 CDT 2016] picard.sam.markduplicates.MarkDuplicates INPUT=[/tmp/BySumOfBaseQAndInOriginalOrderMDTester.6054828717135042634.tmp/input.sam] OUTPUT=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.6054828717135042634.tmp/output.sam METRICS_FILE=/tmp/BySumOfBaseQAndInOriginalOrderMDTester.6054828717135042634.tmp/metrics.txt DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag REMOVE_DUPLICATES=false ASSUME_SORTED=false PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 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 04:11:10 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 04:11:10 MarkDuplicates Start of doWork freeMemory: 1736376800; totalMemory: 1774190592; maxMemory: 1908932608
INFO 2016-08-16 04:11:10 MarkDuplicates Reading input file and constructing read end information.
INFO 2016-08-16 04:11:10 MarkDuplicates Will retain up to 7342048 data points before spilling to disk.
INFO 2016-08-16 04:11:10 MarkDuplicates Read 4 records. 0 pairs never matched.
INFO 2016-08-16 04:11:10 MarkDuplicates After buildSortedReadEndLists freeMemory: 1672887232; totalMemory: 1769472000; maxMemory: 1908932608
INFO 2016-08-16 04:11:10 MarkDuplicates Will retain up to 59654144 duplicate indices before spilling to disk.
INFO 2016-08-16 04:11:10 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2016-08-16 04:11:10 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2016-08-16 04:11:10 MarkDuplicates Sorting list of duplicate records.
INFO 2016-08-16 04:11:11 MarkDuplicates After generateDuplicateIndexes freeMemory: 1257783808; totalMemory: 1773142016; maxMemory: 1908932608
INFO 2016-08-16 04:11:11 MarkDuplicates Marking 2 records as duplicates.
INFO 2016-08-16 04:11:11 MarkDuplicates Found 0 optical duplicate clusters.
INFO 2016-08-16 04:11:11 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2016-08-16 04:11:11 MarkDuplicates Before output close freeMemory: 1735242760; totalMemory: 1773666304; maxMemory: 1908932608
INFO 2016-08-16 04:11:11 MarkDuplicates After output close freeMemory: 1734492536; totalMemory: 1772617728; maxMemory: 1908932608
[Tue Aug 16 04:11:11 CDT 2016] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1772617728