Class picard.sam.markduplicates.EstimateLibraryComplexityTest
Tests
| Test |
Duration |
Result |
| testDefaultMinGroupCount[0](dupes.sam, 0, 0) |
0.021s |
passed |
| testDefaultMinGroupCount[1](big_dupes.sam, 8, 497) |
0.443s |
passed |
| testMaxDiffRate[0](dupes.sam, 0, 2) |
0.021s |
passed |
| testMaxDiffRate[1](big_dupes.sam, 8, 500) |
0.026s |
passed |
| testSimpleDuplicateWithMaxReadLength[0](dupes.sam, 2, 2) |
0.016s |
passed |
| testSimpleDuplicateWithMaxReadLength[1](big_dupes.sam, 512, 500) |
0.026s |
passed |
| testSimpleDuplicate[0](dupes.sam, 2, 2) |
0.023s |
passed |
| testSimpleDuplicate[1](big_dupes.sam, 12, 500) |
0.244s |
passed |
| testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[0](dupes_with_sos.sam, 2, 2) |
0.017s |
passed |
| testSimpleDuplicatesWithSecondaryAndSupplementaryRecords[1](big_dupes_with_sos.sam, 12, 500) |
0.209s |
passed |
Standard error
[Thu Apr 24 13:17:43 EDT 2025] EstimateLibraryComplexity --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam --OUTPUT /tmp/estimateLibraryComplexity1694226383733413493.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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:43 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting.
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1216348160
[Thu Apr 24 13:17:43 EDT 2025] EstimateLibraryComplexity --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam --OUTPUT /tmp/estimateLibraryComplexity14423642234356618337.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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:43 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting.
WARNING 2025-04-24 13:17:43 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name 'H06HDADXX130110:2:1101:10781:2344:1984'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex.
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Finished reading - read 1000 records - moving on to scanning for duplicates.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:17:43 EDT 2025] EstimateLibraryComplexity --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam --OUTPUT /tmp/estimateLibraryComplexity5460979366991856282.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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:43 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting.
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:17:43 EDT 2025] EstimateLibraryComplexity --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam --OUTPUT /tmp/estimateLibraryComplexity608481456103473335.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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:43 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting.
WARNING 2025-04-24 13:17:43 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name 'H06HDADXX130110:2:1101:10781:2344:1984'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex.
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Finished reading - read 1000 records - moving on to scanning for duplicates.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:17:43 EDT 2025] EstimateLibraryComplexity --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam --OUTPUT /tmp/estimateLibraryComplexity6118909063659762544.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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:43 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting.
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:17:43 EDT 2025] EstimateLibraryComplexity --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam --OUTPUT /tmp/estimateLibraryComplexity15901987745127533490.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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:43 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting.
WARNING 2025-04-24 13:17:43 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name 'H06HDADXX130110:2:1101:10781:2344:1984'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex.
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Finished reading - read 1000 records - moving on to scanning for duplicates.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:17:43 EDT 2025] EstimateLibraryComplexity --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/EstimateLibraryComplexity/dupes.sam --OUTPUT /tmp/estimateLibraryComplexity110154710379230591.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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:43 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting.
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:17:43 EDT 2025] EstimateLibraryComplexity --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/EstimateLibraryComplexity/big_dupes.sam --OUTPUT /tmp/estimateLibraryComplexity8567383902403835759.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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:43 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting.
WARNING 2025-04-24 13:17:43 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name 'H06HDADXX130110:2:1101:10781:2344:1984'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex.
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Finished reading - read 1000 records - moving on to scanning for duplicates.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:17:43 EDT 2025] EstimateLibraryComplexity --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/EstimateLibraryComplexity/dupes_with_sos.sam --OUTPUT /tmp/estimateLibraryComplexity9913093871979108854.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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:43 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting.
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Finished reading - read 4 records - moving on to scanning for duplicates.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:17:43 EDT 2025] EstimateLibraryComplexity --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/EstimateLibraryComplexity/big_dupes_with_sos.sam --OUTPUT /tmp/estimateLibraryComplexity16777115013759101628.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 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:17:43 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Will store 2279706 read pairs in memory before sorting.
WARNING 2025-04-24 13:17:43 AbstractOpticalDuplicateFinderCommandLineProgram Default READ_NAME_REGEX '<optimized capture of last three ':' separated fields as numeric values>' did not match read name 'H06HDADXX130110:2:1101:10781:2344:1984'. You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. Note that this message will not be emitted again even if other read names do not match the regex.
INFO 2025-04-24 13:17:43 EstimateLibraryComplexity Finished reading - read 1000 records - moving on to scanning for duplicates.
[Thu Apr 24 13:17:44 EDT 2025] picard.sam.markduplicates.EstimateLibraryComplexity done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824