Class picard.sam.SamErrorMetric.CollectSamErrorMetricsTest

all > picard.sam.SamErrorMetric > CollectSamErrorMetricsTest
186

tests
0

failures
0

ignored
0.194s

duration
100%

successful

Tests

Test Duration Result
parseDirectiveBad[0](ERROR:) 0s passed
parseDirectiveBad[1](ERRORS:READ_ORDINALITY) 0s passed
parseDirectiveBad[2](ERROR;REFERENCE_BASE) 0s passed
parseDirectiveBad[3](ERROR:what) 0.001s passed
parseDirectiveGood[0](ERROR, error_by_all) 0s passed
parseDirectiveGood[10](ERROR:BINNED_HOMOPOLYMER, error_by_binned_length_homopolymer_and_following_ref_base) 0s passed
parseDirectiveGood[11](ERROR:FLOWCELL_TILE, error_by_tile) 0s passed
parseDirectiveGood[12](ERROR:READ_DIRECTION, error_by_read_direction) 0s passed
parseDirectiveGood[13](ERROR:CYCLE, error_by_cycle) 0s passed
parseDirectiveGood[14](ERROR:BINNED_CYCLE, error_by_binned_cycle) 0s passed
parseDirectiveGood[15](ERROR:INSERT_LENGTH, error_by_insert_length) 0s passed
parseDirectiveGood[16](ERROR:BASE_QUALITY, error_by_base_quality) 0s passed
parseDirectiveGood[17](ERROR:MAPPING_QUALITY, error_by_mapping_quality) 0s passed
parseDirectiveGood[18](ERROR:READ_GROUP, error_by_read_group) 0s passed
parseDirectiveGood[19](ERROR:MISMATCHES_IN_READ, error_by_mismatches_in_read) 0s passed
parseDirectiveGood[1](ERROR:ALL, error_by_all) 0s passed
parseDirectiveGood[20](ERROR:ONE_BASE_PADDED_CONTEXT, error_by_one_base_padded_context) 0s passed
parseDirectiveGood[21](ERROR:TWO_BASE_PADDED_CONTEXT, error_by_two_base_padded_context) 0s passed
parseDirectiveGood[22](ERROR:CONSENSUS, error_by_consensus) 0s passed
parseDirectiveGood[23](ERROR:NS_IN_READ, error_by_ns_in_read) 0s passed
parseDirectiveGood[24](ERROR:POST_DINUC:BASE_QUALITY, error_by_post_dinuc_and_base_quality) 0s passed
parseDirectiveGood[25](ERROR:POST_DINUC:BASE_QUALITY:GC_CONTENT, error_by_post_dinuc_and_base_quality_and_gc) 0s passed
parseDirectiveGood[26]( ERROR : POST_DINUC : BASE_QUALITY : GC_CONTENT , error_by_post_dinuc_and_base_quality_and_gc) 0s passed
parseDirectiveGood[27](OVERLAPPING_ERROR, overlapping_error_by_all) 0s passed
parseDirectiveGood[28](OVERLAPPING_ERROR:ALL, overlapping_error_by_all) 0s passed
parseDirectiveGood[29](OVERLAPPING_ERROR:GC_CONTENT, overlapping_error_by_gc) 0s passed
parseDirectiveGood[2](ERROR:GC_CONTENT, error_by_gc) 0s passed
parseDirectiveGood[30](OVERLAPPING_ERROR:READ_ORDINALITY, overlapping_error_by_read_ordinality) 0s passed
parseDirectiveGood[31](OVERLAPPING_ERROR:READ_BASE, overlapping_error_by_read_base) 0s passed
parseDirectiveGood[32](OVERLAPPING_ERROR:REFERENCE_BASE, overlapping_error_by_ref_base) 0s passed
parseDirectiveGood[33](OVERLAPPING_ERROR:PRE_DINUC, overlapping_error_by_pre_dinuc) 0s passed
parseDirectiveGood[34](OVERLAPPING_ERROR:POST_DINUC, overlapping_error_by_post_dinuc) 0s passed
parseDirectiveGood[35](OVERLAPPING_ERROR:HOMOPOLYMER_LENGTH, overlapping_error_by_homopolymer_length) 0s passed
parseDirectiveGood[36](OVERLAPPING_ERROR:HOMOPOLYMER, overlapping_error_by_homopolymer_and_following_ref_base) 0s passed
parseDirectiveGood[37](OVERLAPPING_ERROR:FLOWCELL_TILE, overlapping_error_by_tile) 0s passed
parseDirectiveGood[38](OVERLAPPING_ERROR:READ_DIRECTION, overlapping_error_by_read_direction) 0s passed
parseDirectiveGood[39](OVERLAPPING_ERROR:CYCLE, overlapping_error_by_cycle) 0s passed
parseDirectiveGood[3](ERROR:READ_ORDINALITY, error_by_read_ordinality) 0s passed
parseDirectiveGood[40](OVERLAPPING_ERROR:INSERT_LENGTH, overlapping_error_by_insert_length) 0s passed
parseDirectiveGood[41](OVERLAPPING_ERROR:BASE_QUALITY, overlapping_error_by_base_quality) 0s passed
parseDirectiveGood[4](ERROR:READ_BASE, error_by_read_base) 0s passed
parseDirectiveGood[5](ERROR:REFERENCE_BASE, error_by_ref_base) 0s passed
parseDirectiveGood[6](ERROR:PRE_DINUC, error_by_pre_dinuc) 0s passed
parseDirectiveGood[7](ERROR:POST_DINUC, error_by_post_dinuc) 0s passed
parseDirectiveGood[8](ERROR:HOMOPOLYMER_LENGTH, error_by_homopolymer_length) 0s passed
parseDirectiveGood[9](ERROR:HOMOPOLYMER, error_by_homopolymer_and_following_ref_base) 0s passed
testAggregatorsHaveDistinctSuffixes 0.001s passed
testHasDeletionBeenProcessed[0](1D, [false]) 0s passed
testHasDeletionBeenProcessed[1](2D, [false, true]) 0.001s passed
testHasDeletionBeenProcessed[2](1D1D, [false, true]) 0s passed
testHasDeletionBeenProcessed[3](1D1M1D, [false, false]) 0s passed
testHasDeletionBeenProcessed[4](2D1M1D, [false, true, false]) 0s passed
testHasDeletionBeenProcessed[5](3M2D8M1D, [false, true, false]) 0s passed
testIndelErrors[0]([Ljava.lang.String;@44cb6e72, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 ) 0.009s passed
testIndelErrors[10]([Ljava.lang.String;@2c6619c6, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 4 NUM_DELETED_BASES 8 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 204 ) 0.005s passed
testIndelErrors[11]([Ljava.lang.String;@360b3e3d, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 61 ) 0.005s passed
testIndelErrors[12]([Ljava.lang.String;@32d18431, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 ) 0.005s passed
testIndelErrors[13]([Ljava.lang.String;@2ef42438, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 42 ) 0.004s passed
testIndelErrors[14]([Ljava.lang.String;@34f3565, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 ) 0.004s passed
testIndelErrors[15]([Ljava.lang.String;@7355856d, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 ) 0.006s passed
testIndelErrors[16]([Ljava.lang.String;@533256b3, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 ) 0.005s passed
testIndelErrors[17]([Ljava.lang.String;@14d2c24b, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 22 ) 0.004s passed
testIndelErrors[18]([Ljava.lang.String;@74f72846, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 ) 0.005s passed
testIndelErrors[19]([Ljava.lang.String;@3c4114fe, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 ) 0.004s passed
testIndelErrors[1]([Ljava.lang.String;@79032cf2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 ) 0.006s passed
testIndelErrors[20]([Ljava.lang.String;@4a79eb71, .indel_error_by_indel_length, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 4 ) 0.005s passed
testIndelErrors[21]([Ljava.lang.String;@449c843d, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 ) 0.005s passed
testIndelErrors[22]([Ljava.lang.String;@219c59f9, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 1 ) 0.004s passed
testIndelErrors[23]([Ljava.lang.String;@2ac78ec9, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 ) 0.005s passed
testIndelErrors[24]([Ljava.lang.String;@3b7b0084, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 ) 0.005s passed
testIndelErrors[25]([Ljava.lang.String;@4072506a, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 0 ) 0.005s passed
testIndelErrors[26]([Ljava.lang.String;@7ea14f56, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 ) 0.005s passed
testIndelErrors[27]([Ljava.lang.String;@515ec50c, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 0 ) 0.005s passed
testIndelErrors[28]([Ljava.lang.String;@247d2905, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 ) 0.004s passed
testIndelErrors[29]([Ljava.lang.String;@6bc9e489, .indel_error_by_indel_length, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 3 DELETIONS_Q 0 ERROR_BASES 3 Q_SCORE 0 COVARIATE 3 TOTAL_BASES 0 ) 0.005s passed
testIndelErrors[2]([Ljava.lang.String;@1550a170, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 2 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 ) 0.006s passed
testIndelErrors[30]([Ljava.lang.String;@49d661f1, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 ) 0.005s passed
testIndelErrors[31]([Ljava.lang.String;@4b410841, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 ) 0.004s passed
testIndelErrors[32]([Ljava.lang.String;@48693d44, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 ) 0.004s passed
testIndelErrors[33]([Ljava.lang.String;@56c80793, .indel_error_by_indel_length, NUM_INSERTIONS 1 NUM_INSERTED_BASES 2 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 2 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE 2 TOTAL_BASES 2 ) 0.005s passed
testIndelErrors[3]([Ljava.lang.String;@234151e2, .indel_error_by_all, NUM_INSERTIONS 1 NUM_INSERTED_BASES 1 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 101 ) 0.005s passed
testIndelErrors[4]([Ljava.lang.String;@2fea3c2c, .indel_error_by_all, NUM_INSERTIONS 2 NUM_INSERTED_BASES 4 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 106 ) 0.006s passed
testIndelErrors[5]([Ljava.lang.String;@52dcf034, .indel_error_by_all, NUM_INSERTIONS 4 NUM_INSERTED_BASES 8 INSERTIONS_Q 0 NUM_DELETIONS 0 NUM_DELETED_BASES 0 DELETIONS_Q 0 ERROR_BASES 8 Q_SCORE 0 COVARIATE all TOTAL_BASES 212 ) 0.005s passed
testIndelErrors[6]([Ljava.lang.String;@22bef303, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 ) 0.006s passed
testIndelErrors[7]([Ljava.lang.String;@46203dd7, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 ) 0.005s passed
testIndelErrors[8]([Ljava.lang.String;@35a57b27, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 1 NUM_DELETED_BASES 1 DELETIONS_Q 0 ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 100 ) 0.005s passed
testIndelErrors[9]([Ljava.lang.String;@71496fbe, .indel_error_by_all, NUM_INSERTIONS 0 NUM_INSERTED_BASES 0 INSERTIONS_Q 0 NUM_DELETIONS 2 NUM_DELETED_BASES 4 DELETIONS_Q 0 ERROR_BASES 4 Q_SCORE 0 COVARIATE all TOTAL_BASES 102 ) 0.005s passed
testOneCovariateErrorMetrics[0](.error_by_all, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 49 Q_SCORE 0 COVARIATE all TOTAL_BASES 62 ) 0.001s passed
testOneCovariateErrorMetrics[10](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithIndels.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE 32 TOTAL_BASES 71 ) 0s passed
testOneCovariateErrorMetrics[11](.error_by_all, testdata/picard/sam/BamErrorMetrics/simpleSamWithIndels.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE all TOTAL_BASES 71 ) 0s passed
testOneCovariateErrorMetrics[12](.error_by_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 2,T,A TOTAL_BASES 2 ) 0s passed
testOneCovariateErrorMetrics[13](.error_by_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 3,C,G TOTAL_BASES 1 ) 0.001s passed
testOneCovariateErrorMetrics[14](.error_by_read_ordinality_and_pre_dinuc, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE FIRST,G,T TOTAL_BASES 1 ) 0s passed
testOneCovariateErrorMetrics[15](.error_by_gc, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 0.5 TOTAL_BASES 36 ) 0s passed
testOneCovariateErrorMetrics[16](.error_by_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 10 TOTAL_BASES 2 ) 0s passed
testOneCovariateErrorMetrics[17](.error_by_mapping_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 60 TOTAL_BASES 36 ) 0s passed
testOneCovariateErrorMetrics[18](.error_by_mapping_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE 50 TOTAL_BASES 36 ) 0s passed
testOneCovariateErrorMetrics[19](.error_by_read_group, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 62A40.2 TOTAL_BASES 72 ) 0s passed
testOneCovariateErrorMetrics[1](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 41 Q_SCORE 0 COVARIATE 32 TOTAL_BASES 52 ) 0s passed
testOneCovariateErrorMetrics[20](.error_by_mismatches_in_read, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE -1 TOTAL_BASES 36 ) 0s passed
testOneCovariateErrorMetrics[21](.error_by_mismatches_in_read, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 0 TOTAL_BASES 36 ) 0.001s passed
testOneCovariateErrorMetrics[22](.error_by_one_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE CAG TOTAL_BASES 1 ) 0s passed
testOneCovariateErrorMetrics[23](.error_by_one_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE GTC TOTAL_BASES 1 ) 0s passed
testOneCovariateErrorMetrics[24](.error_by_one_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE CCT TOTAL_BASES 3 ) 0.001s passed
testOneCovariateErrorMetrics[25](.error_by_two_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE ACGGG TOTAL_BASES 1 ) 0s passed
testOneCovariateErrorMetrics[26](.error_by_two_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE GGTCT TOTAL_BASES 1 ) 0s passed
testOneCovariateErrorMetrics[27](.error_by_two_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE CTTGA TOTAL_BASES 1 ) 0.001s passed
testOneCovariateErrorMetrics[28](.error_by_two_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE CCGTG TOTAL_BASES 1 ) 0s passed
testOneCovariateErrorMetrics[29](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE UNKNOWN TOTAL_BASES 72 ) 0s passed
testOneCovariateErrorMetrics[2](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 8 Q_SCORE 0 COVARIATE 33 TOTAL_BASES 10 ) 0s passed
testOneCovariateErrorMetrics[30](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleSingleStrandConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 2 Q_SCORE 0 COVARIATE SIMPLEX_SINGLETON TOTAL_BASES 36 ) 0.001s passed
testOneCovariateErrorMetrics[31](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleSingleStrandConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE SIMPLEX_CONSENSUS TOTAL_BASES 36 ) 0s passed
testOneCovariateErrorMetrics[32](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE DUPLEX_SINGLETON TOTAL_BASES 35 ) 0s passed
testOneCovariateErrorMetrics[33](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 2 Q_SCORE 0 COVARIATE DUPLEX_CONSENSUS TOTAL_BASES 36 ) 0s passed
testOneCovariateErrorMetrics[34](.error_by_ns_in_read, testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 2 Q_SCORE 0 COVARIATE 0 TOTAL_BASES 36 ) 0s passed
testOneCovariateErrorMetrics[35](.error_by_ns_in_read, testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 35 ) 0s passed
testOneCovariateErrorMetrics[36](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE QUINTILE_1 TOTAL_BASES 14 ) 0.001s passed
testOneCovariateErrorMetrics[37](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE QUINTILE_2 TOTAL_BASES 14 ) 0s passed
testOneCovariateErrorMetrics[38](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE QUINTILE_3 TOTAL_BASES 14 ) 0s passed
testOneCovariateErrorMetrics[39](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE QUINTILE_4 TOTAL_BASES 14 ) 0s passed
testOneCovariateErrorMetrics[3](.error_by_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 9,T,T TOTAL_BASES 1 ) 0s passed
testOneCovariateErrorMetrics[40](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE QUINTILE_5 TOTAL_BASES 16 ) 0s passed
testOneCovariateErrorMetrics[4](.error_by_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 2,G,T TOTAL_BASES 2 ) 0s passed
testOneCovariateErrorMetrics[5](.error_by_binned_length_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE SHORT_HOMOPOLYMER,G,T TOTAL_BASES 6 ) 0.001s passed
testOneCovariateErrorMetrics[6](.error_by_read_ordinality_and_pre_dinuc, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 3 Q_SCORE 0 COVARIATE FIRST,A,A TOTAL_BASES 3 ) 0s passed
testOneCovariateErrorMetrics[7](.error_by_all, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 72 ) 0s passed
testOneCovariateErrorMetrics[8](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 32 TOTAL_BASES 51 ) 0s passed
testOneCovariateErrorMetrics[9](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE 33 TOTAL_BASES 21 ) 0s passed
testOneCovariateIndelErrorMetrics[0](.error_by_all, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 49 Q_SCORE 0 COVARIATE all TOTAL_BASES 62 ) 0s passed
testOneCovariateIndelErrorMetrics[10](.error_by_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 2,T,A TOTAL_BASES 2 ) 0s passed
testOneCovariateIndelErrorMetrics[11](.error_by_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 3,C,G TOTAL_BASES 1 ) 0s passed
testOneCovariateIndelErrorMetrics[12](.error_by_read_ordinality_and_pre_dinuc, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE FIRST,G,T TOTAL_BASES 1 ) 0s passed
testOneCovariateIndelErrorMetrics[13](.error_by_gc, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 0.5 TOTAL_BASES 36 ) 0s passed
testOneCovariateIndelErrorMetrics[14](.error_by_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 10 TOTAL_BASES 2 ) 0.001s passed
testOneCovariateIndelErrorMetrics[15](.error_by_mapping_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 60 TOTAL_BASES 36 ) 0s passed
testOneCovariateIndelErrorMetrics[16](.error_by_mapping_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE 50 TOTAL_BASES 36 ) 0s passed
testOneCovariateIndelErrorMetrics[17](.error_by_read_group, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 62A40.2 TOTAL_BASES 72 ) 0.001s passed
testOneCovariateIndelErrorMetrics[18](.error_by_mismatches_in_read, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE -1 TOTAL_BASES 36 ) 0s passed
testOneCovariateIndelErrorMetrics[19](.error_by_mismatches_in_read, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 0 TOTAL_BASES 36 ) 0s passed
testOneCovariateIndelErrorMetrics[1](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 41 Q_SCORE 0 COVARIATE 32 TOTAL_BASES 52 ) 0.001s passed
testOneCovariateIndelErrorMetrics[20](.error_by_one_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE CAG TOTAL_BASES 1 ) 0s passed
testOneCovariateIndelErrorMetrics[21](.error_by_one_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE GTC TOTAL_BASES 1 ) 0.001s passed
testOneCovariateIndelErrorMetrics[22](.error_by_one_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE CCT TOTAL_BASES 3 ) 0s passed
testOneCovariateIndelErrorMetrics[23](.error_by_two_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE ACGGG TOTAL_BASES 1 ) 0s passed
testOneCovariateIndelErrorMetrics[24](.error_by_two_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE GGTCT TOTAL_BASES 1 ) 0.001s passed
testOneCovariateIndelErrorMetrics[25](.error_by_two_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE CTTGA TOTAL_BASES 1 ) 0s passed
testOneCovariateIndelErrorMetrics[26](.error_by_two_base_padded_context, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE CCGTG TOTAL_BASES 1 ) 0s passed
testOneCovariateIndelErrorMetrics[27](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE UNKNOWN TOTAL_BASES 72 ) 0.001s passed
testOneCovariateIndelErrorMetrics[28](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleSingleStrandConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 2 Q_SCORE 0 COVARIATE SIMPLEX_SINGLETON TOTAL_BASES 36 ) 0s passed
testOneCovariateIndelErrorMetrics[29](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleSingleStrandConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE SIMPLEX_CONSENSUS TOTAL_BASES 36 ) 0s passed
testOneCovariateIndelErrorMetrics[2](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 8 Q_SCORE 0 COVARIATE 33 TOTAL_BASES 10 ) 0s passed
testOneCovariateIndelErrorMetrics[30](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE DUPLEX_SINGLETON TOTAL_BASES 35 ) 0s passed
testOneCovariateIndelErrorMetrics[31](.error_by_consensus, testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 2 Q_SCORE 0 COVARIATE DUPLEX_CONSENSUS TOTAL_BASES 36 ) 0s passed
testOneCovariateIndelErrorMetrics[32](.error_by_ns_in_read, testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 2 Q_SCORE 0 COVARIATE 0 TOTAL_BASES 36 ) 0s passed
testOneCovariateIndelErrorMetrics[33](.error_by_ns_in_read, testdata/picard/sam/BamErrorMetrics/simpleDuplexConsensusSamWithBaseErrors.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 1 TOTAL_BASES 35 ) 0s passed
testOneCovariateIndelErrorMetrics[34](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE QUINTILE_1 TOTAL_BASES 14 ) 0s passed
testOneCovariateIndelErrorMetrics[35](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE QUINTILE_2 TOTAL_BASES 14 ) 0s passed
testOneCovariateIndelErrorMetrics[36](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE QUINTILE_3 TOTAL_BASES 14 ) 0s passed
testOneCovariateIndelErrorMetrics[37](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE QUINTILE_4 TOTAL_BASES 14 ) 0s passed
testOneCovariateIndelErrorMetrics[38](.error_by_binned_cycle, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors2.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE QUINTILE_5 TOTAL_BASES 16 ) 0.001s passed
testOneCovariateIndelErrorMetrics[3](.error_by_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 9,T,T TOTAL_BASES 1 ) 0s passed
testOneCovariateIndelErrorMetrics[4](.error_by_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 2,G,T TOTAL_BASES 2 ) 0s passed
testOneCovariateIndelErrorMetrics[5](.error_by_binned_length_homopolymer_and_following_ref_base, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE SHORT_HOMOPOLYMER,G,T TOTAL_BASES 6 ) 0.001s passed
testOneCovariateIndelErrorMetrics[6](.error_by_read_ordinality_and_pre_dinuc, testdata/picard/sam/BamErrorMetrics/chrMReadsWithClips.sam, 30, ERROR_BASES 3 Q_SCORE 0 COVARIATE FIRST,A,A TOTAL_BASES 3 ) 0s passed
testOneCovariateIndelErrorMetrics[7](.error_by_all, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE all TOTAL_BASES 72 ) 0s passed
testOneCovariateIndelErrorMetrics[8](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 1 Q_SCORE 0 COVARIATE 32 TOTAL_BASES 51 ) 0s passed
testOneCovariateIndelErrorMetrics[9](.error_by_base_quality, testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam, 30, ERROR_BASES 0 Q_SCORE 0 COVARIATE 33 TOTAL_BASES 21 ) 0.001s passed
testReadCycleBinError[0](1.0000000000000002) 0.001s passed
testReadCycleBinError[1](-4.9E-324) 0s passed
testReadCycleBinError[2](-1.0) 0s passed
testReadCycleBinError[3](-0.1) 0s passed
testReadCycleBinError[4](1.1) 0s passed
testReadCycleBinError[5](100.0) 0s passed
testReadCycleBin[0](0.0, QUINTILE_1) 0s passed
testReadCycleBin[10](1.0, QUINTILE_5) 0s passed
testReadCycleBin[1](0.2, QUINTILE_1) 0s passed
testReadCycleBin[2](0.20000000000000004, QUINTILE_2) 0s passed
testReadCycleBin[3](0.4, QUINTILE_2) 0s passed
testReadCycleBin[4](0.4000000000000001, QUINTILE_3) 0s passed
testReadCycleBin[5](0.54, QUINTILE_3) 0s passed
testReadCycleBin[6](0.6, QUINTILE_3) 0s passed
testReadCycleBin[7](0.6000000000000001, QUINTILE_4) 0s passed
testReadCycleBin[8](0.8, QUINTILE_4) 0s passed
testReadCycleBin[9](0.8000000000000002, QUINTILE_5) 0s passed
testStratifiersHaveDistinctSuffixes 0.001s passed
testTooManyDirectives 0.001s passed

Standard error

[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels18027459012655142666.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 100 loci, Processed 100 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels857548920143538947.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 100 loci, Processed 100 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels4483107299610675988.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 101 loci, Processed 101 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels13524151989116315239.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 100 loci, Processed 100 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels6956791136268515070.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 102 loci, Processed 102 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels2068564375834610643.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 102 loci, Processed 102 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels17568116078483962355.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 101 loci, Processed 101 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels17145636182401923726.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 101 loci, Processed 101 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels7040134884012112093.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 101 loci, Processed 101 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels1961793993675613516.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 106 loci, Processed 106 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels4885943647661037592.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 106 loci, Processed 106 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels5413056761018668341.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 61 loci, Processed 61 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels4396115090316285674.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 42 loci, Processed 42 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels16536315913813666994.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 42 loci, Processed 42 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels566050860247523108.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 23 loci, Processed 23 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels10806197852842513956.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 22 loci, Processed 22 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels7140455875674705747.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 22 loci, Processed 22 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels12083852178459097261.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 22 loci, Processed 22 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels1790366675362516393.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 100 loci, Processed 100 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels10314975159700255107.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 100 loci, Processed 100 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels17844075772663055207.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 60 loci, Processed 60 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels16899077771473736108.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 11 loci, Processed 11 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels319425105281959155.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 10 loci, Processed 10 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels3649949326263790777.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 101 loci, Processed 101 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels1827400322120407903.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 102 loci, Processed 102 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels14853738258477475785.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 64 loci, Processed 64 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels6209216969529310634.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 11 loci, Processed 11 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels5020171211898966758.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 11 loci, Processed 11 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels1223833037620214804.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 63 loci, Processed 63 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels4780730047377402405.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 63 loci, Processed 63 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels13359305243832805916.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 23 loci, Processed 23 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels9929577160133167655.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 22 loci, Processed 22 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels6432202238373733713.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 4 loci, Processed 4 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT /tmp/Indels11134209904338645924.bam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS INDEL_ERROR --ERROR_METRICS INDEL_ERROR:INDEL_LENGTH --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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 13:04:14	CollectSamErrorMetrics	Getting SamLocusIterator
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Using 2 aggregators.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Starting iteration over loci
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Really starting iteration now.
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Iteration complete, generating metric files
INFO	2025-04-24 13:04:14	CollectSamErrorMetrics	Examined 22 loci, Processed 22 loci, Skipped 0 loci.
Computation took 0 seconds.
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:14 EDT 2025] CollectSamErrorMetrics --INPUT testdata/picard/sam/BamErrorMetrics/simpleSamWithBaseErrors1.sam --OUTPUT /tmp/CollectSamErrorMetricsTest.tmp4635188571344963467/test --ERROR_METRICS ERROR --ERROR_METRICS ERROR:BASE_QUALITY --ERROR_METRICS ERROR:INSERT_LENGTH --ERROR_METRICS ERROR:GC_CONTENT --ERROR_METRICS ERROR:READ_DIRECTION --ERROR_METRICS ERROR:PAIR_ORIENTATION --ERROR_METRICS ERROR:HOMOPOLYMER --ERROR_METRICS ERROR:BINNED_HOMOPOLYMER --ERROR_METRICS ERROR:CYCLE --ERROR_METRICS ERROR:READ_ORDINALITY --ERROR_METRICS ERROR:READ_ORDINALITY:CYCLE --ERROR_METRICS ERROR:READ_ORDINALITY:HOMOPOLYMER --ERROR_METRICS ERROR:READ_ORDINALITY:GC_CONTENT --ERROR_METRICS ERROR:READ_ORDINALITY:PRE_DINUC --ERROR_METRICS ERROR:MAPPING_QUALITY --ERROR_METRICS ERROR:READ_GROUP --ERROR_METRICS ERROR:MISMATCHES_IN_READ --ERROR_METRICS ERROR:ONE_BASE_PADDED_CONTEXT --ERROR_METRICS OVERLAPPING_ERROR --ERROR_METRICS OVERLAPPING_ERROR:BASE_QUALITY --ERROR_METRICS OVERLAPPING_ERROR:INSERT_LENGTH --ERROR_METRICS OVERLAPPING_ERROR:READ_ORDINALITY --ERROR_METRICS OVERLAPPING_ERROR:READ_ORDINALITY:CYCLE --ERROR_METRICS OVERLAPPING_ERROR:READ_ORDINALITY:HOMOPOLYMER --ERROR_METRICS OVERLAPPING_ERROR:READ_ORDINALITY:GC_CONTENT --ERROR_METRICS INDEL_ERROR --ERROR_METRICS ERROR:ALL:GC_CONTENT:READ_ORDINALITY:READ_BASE:READ_DIRECTION:PAIR_ORIENTATION:PAIR_PROPERNESS:REFERENCE_BASE:PRE_DINUC:POST_DINUC:HOMOPOLYMER_LENGTH:HOMOPOLYMER:BINNED_HOMOPOLYMER:FLOWCELL_TILE:FLOWCELL_Y:FLOWCELL_X:READ_GROUP:CYCLE:BINNED_CYCLE:SOFT_CLIPS:INSERT_LENGTH:BASE_QUALITY:MAPPING_QUALITY:MISMATCHES_IN_READ:ONE_BASE_PADDED_CONTEXT:TWO_BASE_PADDED_CONTEXT:CONSENSUS:NS_IN_READ:INSERTIONS_IN_READ:DELETIONS_IN_READ:INDELS_IN_READ:INDEL_LENGTH:ALL --VCF /mounts/lovelace/software/picard/picard/testdata/picard/sam/BamErrorMetrics/NIST.selected.vcf --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MIN_MAPPING_Q 20 --MIN_BASE_Q 20 --PRIOR_Q 30 --MAX_LOCI 0 --LONG_HOMOPOLYMER 6 --LOCATION_BIN_SIZE 2500 --PROBABILITY 1.0 --PROGRESS_STEP_INTERVAL 100000 --INTERVAL_ITERATOR false --FILE_EXTENSION  --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:04:14 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
[Thu Apr 24 13:04:14 EDT 2025] picard.sam.SamErrorMetric.CollectSamErrorMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp