Class picard.analysis.CollectOxoGMetricsTest

all > picard.analysis > CollectOxoGMetricsTest
9

tests
0

failures
0

ignored
0.026s

duration
100%

successful

Tests

Test Duration Result
testCollectOxoGMetrics 0.008s passed
testCollectOxoGMetricsLongContext 0.013s passed
testCollectOxoGMetricsShortContext 0.004s passed
testNegativeCustomCommandLineValidation[0](5, 10, 1, [AAC], Middle base of context sequence AAC must be C) 0.001s passed
testNegativeCustomCommandLineValidation[1](10, 10, 1, [ATCAT, AAGAA], Context AAGAA is not 3 long as implied by CONTEXT_SIZE=1) 0s passed
testNegativeCustomCommandLineValidation[2](10, 5, 1, [ACC], MAXIMUM_INSERT_SIZE cannot be less than MINIMUM_INSERT_SIZE) 0s passed
testNegativeCustomCommandLineValidation[3](-5, 10, 1, [ACC], MINIMUM_INSERT_SIZE cannot be negative) 0s passed
testPositiveCustomCommandLineValidation[0](5, 10, 1, [ACC]) 0s passed
testPositiveCustomCommandLineValidation[1](10, 10, 2, [ATCAT, AACAA]) 0s passed

Standard error

[Thu Apr 24 12:59:24 EDT 2025] CollectOxoGMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test9622944342822125949.oxo_g_metrics --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --MINIMUM_QUALITY_SCORE 20 --MINIMUM_MAPPING_QUALITY 30 --MINIMUM_INSERT_SIZE 60 --MAXIMUM_INSERT_SIZE 600 --INCLUDE_NON_PF_READS true --USE_OQ true --CONTEXT_SIZE 1 --STOP_AFTER 2147483647 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:24 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 12:59:24	CollectOxoGMetrics	Generated 16 context strings.
INFO	2025-04-24 12:59:24	CollectOxoGMetrics	Loading dbSNP File: null
INFO	2025-04-24 12:59:24	CollectOxoGMetrics	Starting iteration.
[Thu Apr 24 12:59:24 EDT 2025] picard.analysis.CollectOxoGMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:24 EDT 2025] CollectOxoGMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test15013444108292760326.oxo_g_metrics --CONTEXT_SIZE 2 --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --MINIMUM_QUALITY_SCORE 20 --MINIMUM_MAPPING_QUALITY 30 --MINIMUM_INSERT_SIZE 60 --MAXIMUM_INSERT_SIZE 600 --INCLUDE_NON_PF_READS true --USE_OQ true --STOP_AFTER 2147483647 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:24 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 12:59:24	CollectOxoGMetrics	Generated 256 context strings.
INFO	2025-04-24 12:59:24	CollectOxoGMetrics	Loading dbSNP File: null
INFO	2025-04-24 12:59:24	CollectOxoGMetrics	Starting iteration.
[Thu Apr 24 12:59:24 EDT 2025] picard.analysis.CollectOxoGMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 12:59:24 EDT 2025] CollectOxoGMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/AlignmentSummaryMetrics/summary_alignment_stats_test.sam --OUTPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/test9291149453138824970.oxo_g_metrics --CONTEXT_SIZE 0 --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --MINIMUM_QUALITY_SCORE 20 --MINIMUM_MAPPING_QUALITY 30 --MINIMUM_INSERT_SIZE 60 --MAXIMUM_INSERT_SIZE 600 --INCLUDE_NON_PF_READS true --USE_OQ true --STOP_AFTER 2147483647 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 12:59:24 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 12:59:24	CollectOxoGMetrics	Generated 1 context strings.
INFO	2025-04-24 12:59:24	CollectOxoGMetrics	Loading dbSNP File: null
INFO	2025-04-24 12:59:24	CollectOxoGMetrics	Starting iteration.
[Thu Apr 24 12:59:24 EDT 2025] picard.analysis.CollectOxoGMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824