Class picard.sam.markduplicates.CheckDuplicateMarkingTest
Tests
| Test |
Duration |
Result |
| testCheckDuplicateMarking[0](pass_queryname.sam, 0) |
0.002s |
passed |
| testCheckDuplicateMarking[1](pass_coordinate.sam, 0) |
0.002s |
passed |
| testCheckDuplicateMarking[2](fail_mate_queryname.sam, 1) |
0.002s |
passed |
| testCheckDuplicateMarking[3](fail_mate_coordinate.sam, 1) |
0.001s |
passed |
| testCheckDuplicateMarking[4](fail_supplementary_queryname_1.sam, 1) |
0.001s |
passed |
| testCheckDuplicateMarking[5](fail_supplementary_coordinate_1.sam, 1) |
0.001s |
passed |
| testCheckDuplicateMarking[6](fail_supplementary_queryname_2.sam, 1) |
0.002s |
passed |
| testCheckDuplicateMarking[7](fail_supplementary_coordinate_2.sam, 1) |
0.001s |
passed |
| testCheckDuplicateMarking[8](fail_secondary_queryname.sam, 1) |
0.001s |
passed |
| testCheckDuplicateMarking[9](fail_secondary_coordinate.sam, 1) |
0.001s |
passed |
Standard error
[Thu Apr 24 13:17:43 EDT 2025] CheckDuplicateMarking --INPUT testdata/picard/sam/CheckDuplicateMarking/pass_queryname.sam --MODE ALL --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --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 CheckDuplicateMarking All records' duplicate markings agree.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1216348160
[Thu Apr 24 13:17:43 EDT 2025] CheckDuplicateMarking --INPUT testdata/picard/sam/CheckDuplicateMarking/pass_coordinate.sam --MODE ALL --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --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 CheckDuplicateMarking Input file isn't queryname sorted. Sorting into temp space.
INFO 2025-04-24 13:17:43 CheckDuplicateMarking All records' duplicate markings agree.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1216348160
[Thu Apr 24 13:17:43 EDT 2025] CheckDuplicateMarking --INPUT testdata/picard/sam/CheckDuplicateMarking/fail_mate_queryname.sam --MODE ALL --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --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
WARNING 2025-04-24 13:17:43 CheckDuplicateMarking Reads with queryname read_28833_29006_6945 have different duplicate flags (at chr20:28993)
ERROR 2025-04-24 13:17:43 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1216348160
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:17:43 EDT 2025] CheckDuplicateMarking --INPUT testdata/picard/sam/CheckDuplicateMarking/fail_mate_coordinate.sam --MODE ALL --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --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 CheckDuplicateMarking Input file isn't queryname sorted. Sorting into temp space.
WARNING 2025-04-24 13:17:43 CheckDuplicateMarking Reads with queryname read_28833_29006_6945 have different duplicate flags (at chr20:28993)
ERROR 2025-04-24 13:17:43 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1216348160
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:17:43 EDT 2025] CheckDuplicateMarking --INPUT testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_queryname_1.sam --MODE ALL --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --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
WARNING 2025-04-24 13:17:43 CheckDuplicateMarking Reads with queryname read_28833_29006_6945 have different duplicate flags (at chr20:18935)
ERROR 2025-04-24 13:17:43 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1216348160
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:17:43 EDT 2025] CheckDuplicateMarking --INPUT testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_coordinate_1.sam --MODE ALL --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --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 CheckDuplicateMarking Input file isn't queryname sorted. Sorting into temp space.
WARNING 2025-04-24 13:17:43 CheckDuplicateMarking Reads with queryname read_28833_29006_6945 have different duplicate flags (at chr20:18935)
ERROR 2025-04-24 13:17:43 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1216348160
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:17:43 EDT 2025] CheckDuplicateMarking --INPUT testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_queryname_2.sam --MODE ALL --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --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
WARNING 2025-04-24 13:17:43 CheckDuplicateMarking Reads with queryname read_28701_28881_323b have different duplicate flags (at chr20:19211)
ERROR 2025-04-24 13:17:43 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1216348160
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:17:43 EDT 2025] CheckDuplicateMarking --INPUT testdata/picard/sam/CheckDuplicateMarking/fail_supplementary_coordinate_2.sam --MODE ALL --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --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 CheckDuplicateMarking Input file isn't queryname sorted. Sorting into temp space.
WARNING 2025-04-24 13:17:43 CheckDuplicateMarking Reads with queryname read_28701_28881_323b have different duplicate flags (at chr20:19211)
ERROR 2025-04-24 13:17:43 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1216348160
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:17:43 EDT 2025] CheckDuplicateMarking --INPUT testdata/picard/sam/CheckDuplicateMarking/fail_secondary_queryname.sam --MODE ALL --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --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
WARNING 2025-04-24 13:17:43 CheckDuplicateMarking Reads with queryname read_28701_28881_323b have different duplicate flags (at chr20:19334)
ERROR 2025-04-24 13:17:43 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1216348160
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:17:43 EDT 2025] CheckDuplicateMarking --INPUT testdata/picard/sam/CheckDuplicateMarking/fail_secondary_coordinate.sam --MODE ALL --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --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 CheckDuplicateMarking Input file isn't queryname sorted. Sorting into temp space.
WARNING 2025-04-24 13:17:43 CheckDuplicateMarking Reads with queryname read_28701_28881_323b have different duplicate flags (at chr20:19334)
ERROR 2025-04-24 13:17:43 CheckDuplicateMarking Found 1 records that do not agree on their duplicate flag.
[Thu Apr 24 13:17:43 EDT 2025] picard.sam.markduplicates.CheckDuplicateMarking done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1216348160
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp