Class picard.sam.markduplicates.EstimateLibraryComplexityTest
Tests
| Test |
Duration |
Result |
| testDefaultMinGroupCount |
0.030s |
passed |
| testMaxDiffRate |
0.027s |
passed |
| testSimpleDuplicate |
0.028s |
passed |
| testSimpleDuplicateWithMaxReadLength |
0.028s |
passed |
| testSimpleDuplicatesWithSecondaryAndSupplementaryRecords |
0.028s |
passed |
Standard error
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity3157012686014658569.els_metrics MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 MIN_GROUP_COUNT=2 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=3098916 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
INFO 2016-08-16 04:11:37 EstimateLibraryComplexity Will store 3098916 read pairs in memory before sorting.
INFO 2016-08-16 04:11:37 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates.
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity4271848629314161831.els_metrics MAX_DIFF_RATE=0.0 MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 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=3098916 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
INFO 2016-08-16 04:11:37 EstimateLibraryComplexity Will store 3098916 read pairs in memory before sorting.
INFO 2016-08-16 04:11:37 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates.
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity3031350548902952578.els_metrics MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 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=3098916 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
INFO 2016-08-16 04:11:37 EstimateLibraryComplexity Will store 3098916 read pairs in memory before sorting.
INFO 2016-08-16 04:11:37 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates.
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam] OUTPUT=/tmp/estimateLibraryComplexity487198145363158553.els_metrics MAX_DIFF_RATE=0.0 MAX_READ_LENGTH=10 MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 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=3098916 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
INFO 2016-08-16 04:11:37 EstimateLibraryComplexity Will store 3098916 read pairs in memory before sorting.
INFO 2016-08-16 04:11:37 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates.
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/EstimateLibraryComplexity/dupes_with_sos.sam] OUTPUT=/tmp/estimateLibraryComplexity7499526266799295772.els_metrics MIN_GROUP_COUNT=1 MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 MAX_READ_LENGTH=0 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=3098916 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
INFO 2016-08-16 04:11:37 EstimateLibraryComplexity Will store 3098916 read pairs in memory before sorting.
INFO 2016-08-16 04:11:37 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates.
[Tue Aug 16 04:11:37 CDT 2016] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1823997952