Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/c444f39fd2c07f29835777fb996303/659_cIX-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/2bddb892927de59c24ae10b95ced8f/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/2bddb892927de59c24ae10b95ced8f/.command.sh
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
==> STAGING COMPLETE (5 inputs)
Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT 659_cIX-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bam --METRICS_FILE 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
00:03:49.524 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
[Thu May 28 00:03:49 GMT 2026] MarkDuplicates --INPUT 659_cIX-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bam --METRICS_FILE 659_cIX-T1-TRNA-1_B23WHTKLT4_1.md.bam.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu May 28 00:03:49 GMT 2026] Executing as ?@nf-902bddb892927de59c24ae10b95ced8f-e1802-84jvp on Linux 6.12.83 amd64; OpenJDK 64-Bit Server VM 17.0.3-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.4.0.0
INFO 2026-05-28 00:03:49 MarkDuplicates Start of doWork freeMemory: 105829168; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-05-28 00:03:49 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-05-28 00:03:49 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-05-28 00:03:53 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:11,925,928
INFO 2026-05-28 00:03:53 MarkDuplicates Tracking 2018 as yet unmatched pairs. 227 records in RAM.
INFO 2026-05-28 00:03:55 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:21,874,700
INFO 2026-05-28 00:03:55 MarkDuplicates Tracking 3572 as yet unmatched pairs. 385 records in RAM.
INFO 2026-05-28 00:03:57 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:31,692,056
INFO 2026-05-28 00:03:57 MarkDuplicates Tracking 5039 as yet unmatched pairs. 447 records in RAM.
INFO 2026-05-28 00:03:59 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:39,479,978
INFO 2026-05-28 00:03:59 MarkDuplicates Tracking 6494 as yet unmatched pairs. 491 records in RAM.
INFO 2026-05-28 00:04:01 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr1:55,162,259
INFO 2026-05-28 00:04:01 MarkDuplicates Tracking 7652 as yet unmatched pairs. 91 records in RAM.
INFO 2026-05-28 00:04:03 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr1:109,923,685
INFO 2026-05-28 00:04:03 MarkDuplicates Tracking 8999 as yet unmatched pairs. 77 records in RAM.
INFO 2026-05-28 00:04:05 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr1:144,436,942
INFO 2026-05-28 00:04:05 MarkDuplicates Tracking 10177 as yet unmatched pairs. 99 records in RAM.
INFO 2026-05-28 00:04:06 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 1s. Last read position: chr1:148,749,045
INFO 2026-05-28 00:04:06 MarkDuplicates Tracking 10713 as yet unmatched pairs. 31 records in RAM.
INFO 2026-05-28 00:04:08 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 1s. Last read position: chr1:150,823,215
INFO 2026-05-28 00:04:08 MarkDuplicates Tracking 12006 as yet unmatched pairs. 242 records in RAM.
INFO 2026-05-28 00:04:09 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr1:153,976,697
INFO 2026-05-28 00:04:09 MarkDuplicates Tracking 14016 as yet unmatched pairs. 911 records in RAM.
INFO 2026-05-28 00:04:11 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr1:155,481,211
INFO 2026-05-28 00:04:11 MarkDuplicates Tracking 14599 as yet unmatched pairs. 135 records in RAM.
INFO 2026-05-28 00:04:13 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr1:156,200,214
INFO 2026-05-28 00:04:13 MarkDuplicates Tracking 16194 as yet unmatched pairs. 54 records in RAM.
INFO 2026-05-28 00:04:15 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 1s. Last read position: chr1:159,833,134
INFO 2026-05-28 00:04:15 MarkDuplicates Tracking 17805 as yet unmatched pairs. 24 records in RAM.
INFO 2026-05-28 00:04:17 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 2s. Last read position: chr1:170,726,344
INFO 2026-05-28 00:04:17 MarkDuplicates Tracking 20394 as yet unmatched pairs. 1217 records in RAM.
INFO 2026-05-28 00:04:19 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chr1:183,633,093
INFO 2026-05-28 00:04:19 MarkDuplicates Tracking 20816 as yet unmatched pairs. 183 records in RAM.
INFO 2026-05-28 00:04:20 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: chr1:201,485,316
INFO 2026-05-28 00:04:20 MarkDuplicates Tracking 26337 as yet unmatched pairs. 4302 records in RAM.
INFO 2026-05-28 00:04:22 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 1s. Last read position: chr1:203,713,163
INFO 2026-05-28 00:04:22 MarkDuplicates Tracking 24089 as yet unmatched pairs. 657 records in RAM.
INFO 2026-05-28 00:04:24 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 2s. Last read position: chr1:215,567,688
INFO 2026-05-28 00:04:24 MarkDuplicates Tracking 24831 as yet unmatched pairs. 64 records in RAM.
INFO 2026-05-28 00:04:26 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:35s. Time for last 1,000,000: 2s. Last read position: chr1:227,759,234
INFO 2026-05-28 00:04:26 MarkDuplicates Tracking 26144 as yet unmatched pairs. 82 records in RAM.
INFO 2026-05-28 00:04:28 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 2s. Last read position: chr1:243,552,785
INFO 2026-05-28 00:04:28 MarkDuplicates Tracking 28365 as yet unmatched pairs. 564 records in RAM.
INFO 2026-05-28 00:04:30 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 1s. Last read position: chr2:24,301,159
INFO 2026-05-28 00:04:30 MarkDuplicates Tracking 29246 as yet unmatched pairs. 29128 records in RAM.
INFO 2026-05-28 00:04:32 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr2:28,799,203
INFO 2026-05-28 00:04:32 MarkDuplicates Tracking 32933 as yet unmatched pairs. 32814 records in RAM.
INFO 2026-05-28 00:04:34 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,406
INFO 2026-05-28 00:04:34 MarkDuplicates Tracking 258889 as yet unmatched pairs. 20431 records in RAM.
INFO 2026-05-28 00:04:36 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 1s. Last read position: chr2:55,049,997
INFO 2026-05-28 00:04:36 MarkDuplicates Tracking 276832 as yet unmatched pairs. 19667 records in RAM.
INFO 2026-05-28 00:04:37 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 1s. Last read position: chr2:73,519,774
INFO 2026-05-28 00:04:37 MarkDuplicates Tracking 274310 as yet unmatched pairs. 17145 records in RAM.
INFO 2026-05-28 00:04:39 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 1s. Last read position: chr2:96,208,309
INFO 2026-05-28 00:04:39 MarkDuplicates Tracking 273138 as yet unmatched pairs. 15972 records in RAM.
INFO 2026-05-28 00:04:41 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr2:109,836,611
INFO 2026-05-28 00:04:41 MarkDuplicates Tracking 271505 as yet unmatched pairs. 14337 records in RAM.
INFO 2026-05-28 00:04:42 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:51s. Time for last 1,000,000: 1s. Last read position: chr2:164,955,213
INFO 2026-05-28 00:04:42 MarkDuplicates Tracking 270204 as yet unmatched pairs. 13028 records in RAM.
INFO 2026-05-28 00:04:44 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 1s. Last read position: chr2:188,999,841
INFO 2026-05-28 00:04:44 MarkDuplicates Tracking 270362 as yet unmatched pairs. 13186 records in RAM.
INFO 2026-05-28 00:04:46 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 2s. Last read position: chr2:206,757,254
INFO 2026-05-28 00:04:46 MarkDuplicates Tracking 267184 as yet unmatched pairs. 10000 records in RAM.
INFO 2026-05-28 00:04:49 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: chr2:215,384,931
INFO 2026-05-28 00:04:49 MarkDuplicates Tracking 267890 as yet unmatched pairs. 10697 records in RAM.
INFO 2026-05-28 00:04:51 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:00s. Time for last 1,000,000: 2s. Last read position: chr2:215,430,808
INFO 2026-05-28 00:04:51 MarkDuplicates Tracking 268180 as yet unmatched pairs. 10975 records in RAM.
INFO 2026-05-28 00:04:52 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr2:217,903,607
INFO 2026-05-28 00:04:52 MarkDuplicates Tracking 264533 as yet unmatched pairs. 7327 records in RAM.
INFO 2026-05-28 00:04:54 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 1s. Last read position: chr2:219,420,938
INFO 2026-05-28 00:04:54 MarkDuplicates Tracking 268161 as yet unmatched pairs. 10955 records in RAM.
INFO 2026-05-28 00:04:56 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 1s. Last read position: chr2:231,161,497
INFO 2026-05-28 00:04:56 MarkDuplicates Tracking 259512 as yet unmatched pairs. 2302 records in RAM.
INFO 2026-05-28 00:04:58 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr2:237,396,763
INFO 2026-05-28 00:04:58 MarkDuplicates Tracking 259059 as yet unmatched pairs. 1849 records in RAM.
INFO 2026-05-28 00:05:00 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr3:11,558,536
INFO 2026-05-28 00:05:00 MarkDuplicates Tracking 256633 as yet unmatched pairs. 13459 records in RAM.
INFO 2026-05-28 00:05:02 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 1s. Last read position: chr3:37,295,067
INFO 2026-05-28 00:05:02 MarkDuplicates Tracking 254899 as yet unmatched pairs. 11710 records in RAM.
INFO 2026-05-28 00:05:03 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr3:47,435,063
INFO 2026-05-28 00:05:03 MarkDuplicates Tracking 253394 as yet unmatched pairs. 10205 records in RAM.
INFO 2026-05-28 00:05:05 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 1s. Last read position: chr3:49,123,791
INFO 2026-05-28 00:05:05 MarkDuplicates Tracking 251974 as yet unmatched pairs. 8782 records in RAM.
INFO 2026-05-28 00:05:07 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:16s. Time for last 1,000,000: 1s. Last read position: chr3:52,525,079
INFO 2026-05-28 00:05:07 MarkDuplicates Tracking 250233 as yet unmatched pairs. 7041 records in RAM.
INFO 2026-05-28 00:05:09 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:18s. Time for last 1,000,000: 1s. Last read position: chr3:73,383,984
INFO 2026-05-28 00:05:09 MarkDuplicates Tracking 249231 as yet unmatched pairs. 6038 records in RAM.
INFO 2026-05-28 00:05:10 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 1s. Last read position: chr3:122,407,332
INFO 2026-05-28 00:05:10 MarkDuplicates Tracking 247671 as yet unmatched pairs. 4477 records in RAM.
INFO 2026-05-28 00:05:12 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: chr3:129,304,765
INFO 2026-05-28 00:05:12 MarkDuplicates Tracking 245988 as yet unmatched pairs. 2789 records in RAM.
INFO 2026-05-28 00:05:15 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: chr3:180,984,669
INFO 2026-05-28 00:05:15 MarkDuplicates Tracking 244554 as yet unmatched pairs. 1342 records in RAM.
INFO 2026-05-28 00:05:16 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 1s. Last read position: chr4:966,759
INFO 2026-05-28 00:05:16 MarkDuplicates Tracking 243140 as yet unmatched pairs. 8223 records in RAM.
INFO 2026-05-28 00:05:18 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 1s. Last read position: chr4:16,505,900
INFO 2026-05-28 00:05:18 MarkDuplicates Tracking 241571 as yet unmatched pairs. 6650 records in RAM.
INFO 2026-05-28 00:05:20 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 2s. Last read position: chr4:54,261,184
INFO 2026-05-28 00:05:20 MarkDuplicates Tracking 240207 as yet unmatched pairs. 5278 records in RAM.
INFO 2026-05-28 00:05:22 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr4:87,494,537
INFO 2026-05-28 00:05:22 MarkDuplicates Tracking 238902 as yet unmatched pairs. 3964 records in RAM.
INFO 2026-05-28 00:05:23 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 1s. Last read position: chr4:119,031,569
INFO 2026-05-28 00:05:23 MarkDuplicates Tracking 240378 as yet unmatched pairs. 5439 records in RAM.
INFO 2026-05-28 00:05:25 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 1s. Last read position: chr4:158,671,701
INFO 2026-05-28 00:05:25 MarkDuplicates Tracking 235954 as yet unmatched pairs. 1012 records in RAM.
INFO 2026-05-28 00:05:27 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:36s. Time for last 1,000,000: 2s. Last read position: chr5:14,143,821
INFO 2026-05-28 00:05:27 MarkDuplicates Tracking 235679 as yet unmatched pairs. 15820 records in RAM.
INFO 2026-05-28 00:05:29 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr5:36,104,068
INFO 2026-05-28 00:05:29 MarkDuplicates Tracking 232878 as yet unmatched pairs. 13015 records in RAM.
INFO 2026-05-28 00:05:31 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr5:68,295,167
INFO 2026-05-28 00:05:31 MarkDuplicates Tracking 231713 as yet unmatched pairs. 11849 records in RAM.
INFO 2026-05-28 00:05:33 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:42s. Time for last 1,000,000: 1s. Last read position: chr5:80,078,102
INFO 2026-05-28 00:05:33 MarkDuplicates Tracking 230380 as yet unmatched pairs. 10509 records in RAM.
INFO 2026-05-28 00:05:35 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:44s. Time for last 1,000,000: 1s. Last read position: chr5:103,005,154
INFO 2026-05-28 00:05:35 MarkDuplicates Tracking 228907 as yet unmatched pairs. 9034 records in RAM.
INFO 2026-05-28 00:05:36 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr5:134,718,121
INFO 2026-05-28 00:05:36 MarkDuplicates Tracking 227496 as yet unmatched pairs. 7622 records in RAM.
INFO 2026-05-28 00:05:38 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 1s. Last read position: chr5:141,182,855
INFO 2026-05-28 00:05:38 MarkDuplicates Tracking 226350 as yet unmatched pairs. 6470 records in RAM.
INFO 2026-05-28 00:05:39 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 1s. Last read position: chr5:150,393,411
INFO 2026-05-28 00:05:39 MarkDuplicates Tracking 224614 as yet unmatched pairs. 4734 records in RAM.
INFO 2026-05-28 00:05:41 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:50s. Time for last 1,000,000: 1s. Last read position: chr5:170,270,891
INFO 2026-05-28 00:05:41 MarkDuplicates Tracking 223068 as yet unmatched pairs. 3186 records in RAM.
INFO 2026-05-28 00:05:43 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 1s. Last read position: chr5:178,204,892
INFO 2026-05-28 00:05:43 MarkDuplicates Tracking 221936 as yet unmatched pairs. 2052 records in RAM.
INFO 2026-05-28 00:05:45 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: chr5:180,791,675
INFO 2026-05-28 00:05:45 MarkDuplicates Tracking 220335 as yet unmatched pairs. 450 records in RAM.
INFO 2026-05-28 00:05:48 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 2s. Last read position: chr6:30,489,910
INFO 2026-05-28 00:05:48 MarkDuplicates Tracking 218886 as yet unmatched pairs. 11167 records in RAM.
INFO 2026-05-28 00:05:49 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 1s. Last read position: chr6:32,016,065
INFO 2026-05-28 00:05:49 MarkDuplicates Tracking 218125 as yet unmatched pairs. 10401 records in RAM.
INFO 2026-05-28 00:05:51 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 1s. Last read position: chr6:42,641,625
INFO 2026-05-28 00:05:51 MarkDuplicates Tracking 216072 as yet unmatched pairs. 8338 records in RAM.
INFO 2026-05-28 00:05:52 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 1s. Last read position: chr6:75,097,277
INFO 2026-05-28 00:05:52 MarkDuplicates Tracking 215099 as yet unmatched pairs. 7363 records in RAM.
INFO 2026-05-28 00:05:54 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 1s. Last read position: chr6:109,448,786
INFO 2026-05-28 00:05:54 MarkDuplicates Tracking 213379 as yet unmatched pairs. 5641 records in RAM.
INFO 2026-05-28 00:05:55 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr6:132,328,477
INFO 2026-05-28 00:05:55 MarkDuplicates Tracking 212069 as yet unmatched pairs. 4319 records in RAM.
INFO 2026-05-28 00:05:57 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr6:151,366,564
INFO 2026-05-28 00:05:57 MarkDuplicates Tracking 210646 as yet unmatched pairs. 2895 records in RAM.
INFO 2026-05-28 00:05:58 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 1s. Last read position: chr6:159,684,868
INFO 2026-05-28 00:05:58 MarkDuplicates Tracking 210026 as yet unmatched pairs. 2271 records in RAM.
INFO 2026-05-28 00:06:00 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr7:838,883
INFO 2026-05-28 00:06:00 MarkDuplicates Tracking 207845 as yet unmatched pairs. 16861 records in RAM.
INFO 2026-05-28 00:06:03 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:12s. Time for last 1,000,000: 2s. Last read position: chr7:5,528,561
INFO 2026-05-28 00:06:03 MarkDuplicates Tracking 209952 as yet unmatched pairs. 18967 records in RAM.
INFO 2026-05-28 00:06:05 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr7:30,014,819
INFO 2026-05-28 00:06:05 MarkDuplicates Tracking 204444 as yet unmatched pairs. 13457 records in RAM.
INFO 2026-05-28 00:06:06 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr7:47,304,908
INFO 2026-05-28 00:06:06 MarkDuplicates Tracking 203190 as yet unmatched pairs. 12196 records in RAM.
INFO 2026-05-28 00:06:08 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:17s. Time for last 1,000,000: 1s. Last read position: chr7:75,187,246
INFO 2026-05-28 00:06:08 MarkDuplicates Tracking 201779 as yet unmatched pairs. 10779 records in RAM.
INFO 2026-05-28 00:06:09 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr7:92,079,089
INFO 2026-05-28 00:06:09 MarkDuplicates Tracking 200120 as yet unmatched pairs. 9119 records in RAM.
INFO 2026-05-28 00:06:11 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr7:94,430,247
INFO 2026-05-28 00:06:11 MarkDuplicates Tracking 199525 as yet unmatched pairs. 8516 records in RAM.
INFO 2026-05-28 00:06:12 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 1s. Last read position: chr7:102,201,370
INFO 2026-05-28 00:06:12 MarkDuplicates Tracking 197622 as yet unmatched pairs. 6605 records in RAM.
INFO 2026-05-28 00:06:14 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr7:123,542,127
INFO 2026-05-28 00:06:14 MarkDuplicates Tracking 196238 as yet unmatched pairs. 5208 records in RAM.
INFO 2026-05-28 00:06:15 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:24s. Time for last 1,000,000: 1s. Last read position: chr7:130,387,855
INFO 2026-05-28 00:06:15 MarkDuplicates Tracking 194504 as yet unmatched pairs. 3474 records in RAM.
INFO 2026-05-28 00:06:17 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:26s. Time for last 1,000,000: 1s. Last read position: chr7:140,783,022
INFO 2026-05-28 00:06:17 MarkDuplicates Tracking 193561 as yet unmatched pairs. 2527 records in RAM.
INFO 2026-05-28 00:06:19 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 2s. Last read position: chr7:155,302,814
INFO 2026-05-28 00:06:19 MarkDuplicates Tracking 191653 as yet unmatched pairs. 614 records in RAM.
INFO 2026-05-28 00:06:21 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:30s. Time for last 1,000,000: 1s. Last read position: chr8:22,249,092
INFO 2026-05-28 00:06:21 MarkDuplicates Tracking 190206 as yet unmatched pairs. 10533 records in RAM.
INFO 2026-05-28 00:06:22 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr8:38,232,989
INFO 2026-05-28 00:06:22 MarkDuplicates Tracking 188534 as yet unmatched pairs. 8861 records in RAM.
INFO 2026-05-28 00:06:24 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr8:47,863,567
INFO 2026-05-28 00:06:24 MarkDuplicates Tracking 187417 as yet unmatched pairs. 7741 records in RAM.
INFO 2026-05-28 00:06:26 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: chr8:81,680,703
INFO 2026-05-28 00:06:26 MarkDuplicates Tracking 185648 as yet unmatched pairs. 5960 records in RAM.
INFO 2026-05-28 00:06:27 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: chr8:103,371,673
INFO 2026-05-28 00:06:27 MarkDuplicates Tracking 184587 as yet unmatched pairs. 4895 records in RAM.
INFO 2026-05-28 00:06:30 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: chr8:140,739,043
INFO 2026-05-28 00:06:30 MarkDuplicates Tracking 182742 as yet unmatched pairs. 3049 records in RAM.
INFO 2026-05-28 00:06:31 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:02:40s. Time for last 1,000,000: 1s. Last read position: chr8:144,084,854
INFO 2026-05-28 00:06:31 MarkDuplicates Tracking 181082 as yet unmatched pairs. 1389 records in RAM.
INFO 2026-05-28 00:06:33 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:02:42s. Time for last 1,000,000: 1s. Last read position: chr9:27,185,594
INFO 2026-05-28 00:06:33 MarkDuplicates Tracking 179064 as yet unmatched pairs. 12667 records in RAM.
INFO 2026-05-28 00:06:35 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 1s. Last read position: chr9:37,885,980
INFO 2026-05-28 00:06:35 MarkDuplicates Tracking 177578 as yet unmatched pairs. 11179 records in RAM.
INFO 2026-05-28 00:06:37 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 1s. Last read position: chr9:83,971,269
INFO 2026-05-28 00:06:37 MarkDuplicates Tracking 176606 as yet unmatched pairs. 10207 records in RAM.
INFO 2026-05-28 00:06:38 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 1s. Last read position: chr9:98,244,001
INFO 2026-05-28 00:06:38 MarkDuplicates Tracking 174737 as yet unmatched pairs. 8331 records in RAM.
INFO 2026-05-28 00:06:40 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 1s. Last read position: chr9:113,459,615
INFO 2026-05-28 00:06:40 MarkDuplicates Tracking 173173 as yet unmatched pairs. 6765 records in RAM.
INFO 2026-05-28 00:06:42 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:02:51s. Time for last 1,000,000: 1s. Last read position: chr9:122,998,595
INFO 2026-05-28 00:06:42 MarkDuplicates Tracking 171697 as yet unmatched pairs. 5288 records in RAM.
INFO 2026-05-28 00:06:43 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 1s. Last read position: chr9:128,741,624
INFO 2026-05-28 00:06:43 MarkDuplicates Tracking 170414 as yet unmatched pairs. 4001 records in RAM.
INFO 2026-05-28 00:06:45 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 1s. Last read position: chr9:134,053,418
INFO 2026-05-28 00:06:45 MarkDuplicates Tracking 168813 as yet unmatched pairs. 2395 records in RAM.
INFO 2026-05-28 00:06:47 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr9:137,214,634
INFO 2026-05-28 00:06:47 MarkDuplicates Tracking 166977 as yet unmatched pairs. 559 records in RAM.
INFO 2026-05-28 00:06:49 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 2s. Last read position: chr10:17,236,311
INFO 2026-05-28 00:06:49 MarkDuplicates Tracking 166316 as yet unmatched pairs. 10158 records in RAM.
INFO 2026-05-28 00:06:51 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr10:35,179,164
INFO 2026-05-28 00:06:51 MarkDuplicates Tracking 164101 as yet unmatched pairs. 7943 records in RAM.
INFO 2026-05-28 00:06:53 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr10:71,284,839
INFO 2026-05-28 00:06:53 MarkDuplicates Tracking 162873 as yet unmatched pairs. 6715 records in RAM.
INFO 2026-05-28 00:06:55 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 2s. Last read position: chr10:79,298,408
INFO 2026-05-28 00:06:55 MarkDuplicates Tracking 161239 as yet unmatched pairs. 5081 records in RAM.
INFO 2026-05-28 00:06:57 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: chr10:94,403,225
INFO 2026-05-28 00:06:57 MarkDuplicates Tracking 159915 as yet unmatched pairs. 3755 records in RAM.
INFO 2026-05-28 00:06:59 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr10:102,878,458
INFO 2026-05-28 00:06:59 MarkDuplicates Tracking 158267 as yet unmatched pairs. 2105 records in RAM.
INFO 2026-05-28 00:07:01 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 1s. Last read position: chr10:124,983,480
INFO 2026-05-28 00:07:01 MarkDuplicates Tracking 156805 as yet unmatched pairs. 636 records in RAM.
INFO 2026-05-28 00:07:03 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 1s. Last read position: chr11:993,914
INFO 2026-05-28 00:07:03 MarkDuplicates Tracking 155228 as yet unmatched pairs. 19861 records in RAM.
INFO 2026-05-28 00:07:05 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:14s. Time for last 1,000,000: 1s. Last read position: chr11:6,631,184
INFO 2026-05-28 00:07:05 MarkDuplicates Tracking 153523 as yet unmatched pairs. 18156 records in RAM.
INFO 2026-05-28 00:07:06 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 1s. Last read position: chr11:13,727,660
INFO 2026-05-28 00:07:06 MarkDuplicates Tracking 152035 as yet unmatched pairs. 16668 records in RAM.
INFO 2026-05-28 00:07:08 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 1s. Last read position: chr11:46,682,093
INFO 2026-05-28 00:07:08 MarkDuplicates Tracking 150956 as yet unmatched pairs. 15588 records in RAM.
INFO 2026-05-28 00:07:09 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 1s. Last read position: chr11:61,429,197
INFO 2026-05-28 00:07:09 MarkDuplicates Tracking 149071 as yet unmatched pairs. 13698 records in RAM.
INFO 2026-05-28 00:07:11 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 1s. Last read position: chr11:62,559,736
INFO 2026-05-28 00:07:11 MarkDuplicates Tracking 148803 as yet unmatched pairs. 13430 records in RAM.
INFO 2026-05-28 00:07:13 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 1s. Last read position: chr11:64,909,010
INFO 2026-05-28 00:07:13 MarkDuplicates Tracking 146205 as yet unmatched pairs. 10824 records in RAM.
INFO 2026-05-28 00:07:14 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr11:66,055,538
INFO 2026-05-28 00:07:14 MarkDuplicates Tracking 144438 as yet unmatched pairs. 9051 records in RAM.
INFO 2026-05-28 00:07:16 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 1s. Last read position: chr11:69,643,086
INFO 2026-05-28 00:07:16 MarkDuplicates Tracking 143895 as yet unmatched pairs. 8508 records in RAM.
INFO 2026-05-28 00:07:17 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr11:75,402,361
INFO 2026-05-28 00:07:17 MarkDuplicates Tracking 141883 as yet unmatched pairs. 6496 records in RAM.
INFO 2026-05-28 00:07:19 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:03:28s. Time for last 1,000,000: 2s. Last read position: chr11:102,162,500
INFO 2026-05-28 00:07:19 MarkDuplicates Tracking 140725 as yet unmatched pairs. 5338 records in RAM.
INFO 2026-05-28 00:07:21 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr11:117,098,153
INFO 2026-05-28 00:07:21 MarkDuplicates Tracking 138076 as yet unmatched pairs. 2688 records in RAM.
INFO 2026-05-28 00:07:22 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 1s. Last read position: chr11:119,311,932
INFO 2026-05-28 00:07:22 MarkDuplicates Tracking 136813 as yet unmatched pairs. 1425 records in RAM.
INFO 2026-05-28 00:07:24 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr12:1,444,665
INFO 2026-05-28 00:07:24 MarkDuplicates Tracking 135237 as yet unmatched pairs. 16754 records in RAM.
INFO 2026-05-28 00:07:26 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 2s. Last read position: chr12:6,944,562
INFO 2026-05-28 00:07:26 MarkDuplicates Tracking 134177 as yet unmatched pairs. 15689 records in RAM.
INFO 2026-05-28 00:07:28 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 1s. Last read position: chr12:9,093,500
INFO 2026-05-28 00:07:28 MarkDuplicates Tracking 133830 as yet unmatched pairs. 15339 records in RAM.
INFO 2026-05-28 00:07:30 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 1s. Last read position: chr12:19,500,191
INFO 2026-05-28 00:07:30 MarkDuplicates Tracking 131243 as yet unmatched pairs. 12751 records in RAM.
INFO 2026-05-28 00:07:32 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:03:41s. Time for last 1,000,000: 2s. Last read position: chr12:49,127,833
INFO 2026-05-28 00:07:32 MarkDuplicates Tracking 129960 as yet unmatched pairs. 11466 records in RAM.
INFO 2026-05-28 00:07:34 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 1s. Last read position: chr12:54,397,421
INFO 2026-05-28 00:07:34 MarkDuplicates Tracking 128501 as yet unmatched pairs. 10000 records in RAM.
INFO 2026-05-28 00:07:35 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 1s. Last read position: chr12:56,719,991
INFO 2026-05-28 00:07:35 MarkDuplicates Tracking 127020 as yet unmatched pairs. 8519 records in RAM.
INFO 2026-05-28 00:07:37 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:03:46s. Time for last 1,000,000: 1s. Last read position: chr12:57,720,789
INFO 2026-05-28 00:07:37 MarkDuplicates Tracking 125629 as yet unmatched pairs. 7128 records in RAM.
INFO 2026-05-28 00:07:39 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 1s. Last read position: chr12:88,194,953
INFO 2026-05-28 00:07:39 MarkDuplicates Tracking 124192 as yet unmatched pairs. 5691 records in RAM.
INFO 2026-05-28 00:07:40 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 1s. Last read position: chr12:108,523,543
INFO 2026-05-28 00:07:40 MarkDuplicates Tracking 122788 as yet unmatched pairs. 4287 records in RAM.
INFO 2026-05-28 00:07:41 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:03:50s. Time for last 1,000,000: 1s. Last read position: chr12:115,996,528
INFO 2026-05-28 00:07:41 MarkDuplicates Tracking 121512 as yet unmatched pairs. 3010 records in RAM.
INFO 2026-05-28 00:07:43 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: chr12:123,937,325
INFO 2026-05-28 00:07:43 MarkDuplicates Tracking 119817 as yet unmatched pairs. 1314 records in RAM.
INFO 2026-05-28 00:07:45 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 1s. Last read position: chr13:23,338,830
INFO 2026-05-28 00:07:45 MarkDuplicates Tracking 118317 as yet unmatched pairs. 4773 records in RAM.
INFO 2026-05-28 00:07:46 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 1s. Last read position: chr13:48,258,890
INFO 2026-05-28 00:07:46 MarkDuplicates Tracking 117154 as yet unmatched pairs. 3609 records in RAM.
INFO 2026-05-28 00:07:48 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: chr13:110,187,297
INFO 2026-05-28 00:07:48 MarkDuplicates Tracking 115712 as yet unmatched pairs. 2166 records in RAM.
INFO 2026-05-28 00:07:49 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 1s. Last read position: chr13:114,325,372
INFO 2026-05-28 00:07:49 MarkDuplicates Tracking 113615 as yet unmatched pairs. 67 records in RAM.
INFO 2026-05-28 00:07:51 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr14:31,025,976
INFO 2026-05-28 00:07:51 MarkDuplicates Tracking 112128 as yet unmatched pairs. 5344 records in RAM.
INFO 2026-05-28 00:07:52 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: chr14:67,352,978
INFO 2026-05-28 00:07:52 MarkDuplicates Tracking 110799 as yet unmatched pairs. 4009 records in RAM.
INFO 2026-05-28 00:07:54 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 1s. Last read position: chr14:89,350,795
INFO 2026-05-28 00:07:54 MarkDuplicates Tracking 109394 as yet unmatched pairs. 2601 records in RAM.
INFO 2026-05-28 00:07:55 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 1s. Last read position: chr14:103,687,276
INFO 2026-05-28 00:07:55 MarkDuplicates Tracking 107910 as yet unmatched pairs. 1113 records in RAM.
INFO 2026-05-28 00:07:57 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 1s. Last read position: chr15:28,280,207
INFO 2026-05-28 00:07:57 MarkDuplicates Tracking 106367 as yet unmatched pairs. 9789 records in RAM.
INFO 2026-05-28 00:07:59 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:04:08s. Time for last 1,000,000: 2s. Last read position: chr15:38,358,288
INFO 2026-05-28 00:07:59 MarkDuplicates Tracking 104942 as yet unmatched pairs. 8362 records in RAM.
INFO 2026-05-28 00:08:00 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 1s. Last read position: chr15:43,527,116
INFO 2026-05-28 00:08:00 MarkDuplicates Tracking 103623 as yet unmatched pairs. 7043 records in RAM.
INFO 2026-05-28 00:08:02 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 1s. Last read position: chr15:59,137,394
INFO 2026-05-28 00:08:02 MarkDuplicates Tracking 102272 as yet unmatched pairs. 5692 records in RAM.
INFO 2026-05-28 00:08:04 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:04:13s. Time for last 1,000,000: 2s. Last read position: chr15:66,502,655
INFO 2026-05-28 00:08:04 MarkDuplicates Tracking 101514 as yet unmatched pairs. 4934 records in RAM.
INFO 2026-05-28 00:08:06 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 1s. Last read position: chr15:75,688,663
INFO 2026-05-28 00:08:06 MarkDuplicates Tracking 99564 as yet unmatched pairs. 2983 records in RAM.
INFO 2026-05-28 00:08:07 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:04:16s. Time for last 1,000,000: 1s. Last read position: chr15:88,856,432
INFO 2026-05-28 00:08:07 MarkDuplicates Tracking 97899 as yet unmatched pairs. 1318 records in RAM.
INFO 2026-05-28 00:08:09 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 1s. Last read position: chr15:101,971,988
INFO 2026-05-28 00:08:09 MarkDuplicates Tracking 96678 as yet unmatched pairs. 94 records in RAM.
INFO 2026-05-28 00:08:10 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:04:19s. Time for last 1,000,000: 1s. Last read position: chr16:2,090,076
INFO 2026-05-28 00:08:10 MarkDuplicates Tracking 95274 as yet unmatched pairs. 14312 records in RAM.
INFO 2026-05-28 00:08:12 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:04:21s. Time for last 1,000,000: 1s. Last read position: chr16:3,686,075
INFO 2026-05-28 00:08:12 MarkDuplicates Tracking 92886 as yet unmatched pairs. 11922 records in RAM.
INFO 2026-05-28 00:08:13 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 1s. Last read position: chr16:15,080,001
INFO 2026-05-28 00:08:13 MarkDuplicates Tracking 91609 as yet unmatched pairs. 10645 records in RAM.
INFO 2026-05-28 00:08:15 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 1s. Last read position: chr16:15,750,205
INFO 2026-05-28 00:08:15 MarkDuplicates Tracking 93458 as yet unmatched pairs. 12494 records in RAM.
INFO 2026-05-28 00:08:16 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 1s. Last read position: chr16:18,358,430
INFO 2026-05-28 00:08:16 MarkDuplicates Tracking 89637 as yet unmatched pairs. 8673 records in RAM.
INFO 2026-05-28 00:08:17 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 1s. Last read position: chr16:23,069,115
INFO 2026-05-28 00:08:17 MarkDuplicates Tracking 88584 as yet unmatched pairs. 7620 records in RAM.
INFO 2026-05-28 00:08:19 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr16:29,840,285
INFO 2026-05-28 00:08:19 MarkDuplicates Tracking 87376 as yet unmatched pairs. 6412 records in RAM.
INFO 2026-05-28 00:08:20 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 1s. Last read position: chr16:31,183,809
INFO 2026-05-28 00:08:20 MarkDuplicates Tracking 86188 as yet unmatched pairs. 5223 records in RAM.
INFO 2026-05-28 00:08:21 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:04:30s. Time for last 1,000,000: 1s. Last read position: chr16:57,997,644
INFO 2026-05-28 00:08:21 MarkDuplicates Tracking 84004 as yet unmatched pairs. 3039 records in RAM.
INFO 2026-05-28 00:08:23 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 1s. Last read position: chr16:74,874,270
INFO 2026-05-28 00:08:23 MarkDuplicates Tracking 82486 as yet unmatched pairs. 1519 records in RAM.
INFO 2026-05-28 00:08:25 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 1s. Last read position: chr17:1,345,358
INFO 2026-05-28 00:08:25 MarkDuplicates Tracking 80982 as yet unmatched pairs. 27219 records in RAM.
INFO 2026-05-28 00:08:26 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:04:35s. Time for last 1,000,000: 1s. Last read position: chr17:4,939,148
INFO 2026-05-28 00:08:26 MarkDuplicates Tracking 79205 as yet unmatched pairs. 25442 records in RAM.
INFO 2026-05-28 00:08:27 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:04:36s. Time for last 1,000,000: 1s. Last read position: chr17:7,601,465
INFO 2026-05-28 00:08:27 MarkDuplicates Tracking 77709 as yet unmatched pairs. 23944 records in RAM.
INFO 2026-05-28 00:08:29 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:04:38s. Time for last 1,000,000: 1s. Last read position: chr17:16,382,018
INFO 2026-05-28 00:08:29 MarkDuplicates Tracking 77731 as yet unmatched pairs. 23966 records in RAM.
INFO 2026-05-28 00:08:31 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:04:40s. Time for last 1,000,000: 1s. Last read position: chr17:27,577,577
INFO 2026-05-28 00:08:31 MarkDuplicates Tracking 74637 as yet unmatched pairs. 20872 records in RAM.
INFO 2026-05-28 00:08:32 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 1s. Last read position: chr17:35,817,715
INFO 2026-05-28 00:08:32 MarkDuplicates Tracking 73857 as yet unmatched pairs. 20092 records in RAM.
INFO 2026-05-28 00:08:34 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:04:43s. Time for last 1,000,000: 1s. Last read position: chr17:40,273,965
INFO 2026-05-28 00:08:34 MarkDuplicates Tracking 71851 as yet unmatched pairs. 18086 records in RAM.
INFO 2026-05-28 00:08:36 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 1s. Last read position: chr17:43,021,979
INFO 2026-05-28 00:08:36 MarkDuplicates Tracking 71317 as yet unmatched pairs. 17543 records in RAM.
INFO 2026-05-28 00:08:37 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:04:46s. Time for last 1,000,000: 1s. Last read position: chr17:49,404,957
INFO 2026-05-28 00:08:37 MarkDuplicates Tracking 69262 as yet unmatched pairs. 15488 records in RAM.
INFO 2026-05-28 00:08:39 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:04:48s. Time for last 1,000,000: 1s. Last read position: chr17:50,188,563
INFO 2026-05-28 00:08:39 MarkDuplicates Tracking 82693 as yet unmatched pairs. 28918 records in RAM.
INFO 2026-05-28 00:08:41 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:04:50s. Time for last 1,000,000: 2s. Last read position: chr17:50,190,586
INFO 2026-05-28 00:08:41 MarkDuplicates Tracking 71291 as yet unmatched pairs. 17516 records in RAM.
INFO 2026-05-28 00:08:43 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,348
INFO 2026-05-28 00:08:43 MarkDuplicates Tracking 81778 as yet unmatched pairs. 28002 records in RAM.
INFO 2026-05-28 00:08:45 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:04:54s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,187
INFO 2026-05-28 00:08:45 MarkDuplicates Tracking 90093 as yet unmatched pairs. 36317 records in RAM.
INFO 2026-05-28 00:08:47 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 1s. Last read position: chr17:50,199,876
INFO 2026-05-28 00:08:47 MarkDuplicates Tracking 64945 as yet unmatched pairs. 11169 records in RAM.
INFO 2026-05-28 00:08:48 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:04:57s. Time for last 1,000,000: 1s. Last read position: chr17:61,405,593
INFO 2026-05-28 00:08:48 MarkDuplicates Tracking 59681 as yet unmatched pairs. 5905 records in RAM.
INFO 2026-05-28 00:08:49 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:04:58s. Time for last 1,000,000: 1s. Last read position: chr17:75,003,380
INFO 2026-05-28 00:08:49 MarkDuplicates Tracking 57681 as yet unmatched pairs. 3905 records in RAM.
INFO 2026-05-28 00:08:51 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:05:00s. Time for last 1,000,000: 1s. Last read position: chr17:80,105,819
INFO 2026-05-28 00:08:51 MarkDuplicates Tracking 56080 as yet unmatched pairs. 2304 records in RAM.
INFO 2026-05-28 00:08:52 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 1s. Last read position: chr17:82,089,091
INFO 2026-05-28 00:08:52 MarkDuplicates Tracking 54373 as yet unmatched pairs. 597 records in RAM.
INFO 2026-05-28 00:08:54 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 1s. Last read position: chr18:21,704,532
INFO 2026-05-28 00:08:54 MarkDuplicates Tracking 52673 as yet unmatched pairs. 3234 records in RAM.
INFO 2026-05-28 00:08:56 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 1s. Last read position: chr18:49,097,464
INFO 2026-05-28 00:08:56 MarkDuplicates Tracking 51218 as yet unmatched pairs. 1778 records in RAM.
INFO 2026-05-28 00:08:57 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:05:06s. Time for last 1,000,000: 1s. Last read position: chr18:79,973,746
INFO 2026-05-28 00:08:57 MarkDuplicates Tracking 49723 as yet unmatched pairs. 283 records in RAM.
INFO 2026-05-28 00:08:59 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:05:08s. Time for last 1,000,000: 1s. Last read position: chr19:1,823,612
INFO 2026-05-28 00:08:59 MarkDuplicates Tracking 47915 as yet unmatched pairs. 20111 records in RAM.
INFO 2026-05-28 00:09:00 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:05:09s. Time for last 1,000,000: 1s. Last read position: chr19:4,429,540
INFO 2026-05-28 00:09:00 MarkDuplicates Tracking 45941 as yet unmatched pairs. 18136 records in RAM.
INFO 2026-05-28 00:09:02 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:05:11s. Time for last 1,000,000: 1s. Last read position: chr19:7,856,022
INFO 2026-05-28 00:09:02 MarkDuplicates Tracking 44196 as yet unmatched pairs. 16391 records in RAM.
INFO 2026-05-28 00:09:03 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:05:12s. Time for last 1,000,000: 1s. Last read position: chr19:11,193,383
INFO 2026-05-28 00:09:03 MarkDuplicates Tracking 44616 as yet unmatched pairs. 16811 records in RAM.
INFO 2026-05-28 00:09:05 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:05:14s. Time for last 1,000,000: 1s. Last read position: chr19:13,813,050
INFO 2026-05-28 00:09:05 MarkDuplicates Tracking 40873 as yet unmatched pairs. 13068 records in RAM.
INFO 2026-05-28 00:09:08 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 2s. Last read position: chr19:15,257,039
INFO 2026-05-28 00:09:08 MarkDuplicates Tracking 39721 as yet unmatched pairs. 11916 records in RAM.
INFO 2026-05-28 00:09:10 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:05:19s. Time for last 1,000,000: 1s. Last read position: chr19:18,166,237
INFO 2026-05-28 00:09:10 MarkDuplicates Tracking 37579 as yet unmatched pairs. 9772 records in RAM.
INFO 2026-05-28 00:09:11 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 1s. Last read position: chr19:35,269,110
INFO 2026-05-28 00:09:11 MarkDuplicates Tracking 35882 as yet unmatched pairs. 8075 records in RAM.
INFO 2026-05-28 00:09:13 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 1s. Last read position: chr19:40,609,554
INFO 2026-05-28 00:09:13 MarkDuplicates Tracking 34118 as yet unmatched pairs. 6311 records in RAM.
INFO 2026-05-28 00:09:14 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 1s. Last read position: chr19:45,771,655
INFO 2026-05-28 00:09:14 MarkDuplicates Tracking 32787 as yet unmatched pairs. 4980 records in RAM.
INFO 2026-05-28 00:09:15 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 1s. Last read position: chr19:49,497,201
INFO 2026-05-28 00:09:15 MarkDuplicates Tracking 31565 as yet unmatched pairs. 3758 records in RAM.
INFO 2026-05-28 00:09:17 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 1s. Last read position: chr19:55,499,901
INFO 2026-05-28 00:09:17 MarkDuplicates Tracking 28895 as yet unmatched pairs. 1088 records in RAM.
INFO 2026-05-28 00:09:18 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 1s. Last read position: chr20:4,873,962
INFO 2026-05-28 00:09:18 MarkDuplicates Tracking 27016 as yet unmatched pairs. 6066 records in RAM.
INFO 2026-05-28 00:09:20 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:05:29s. Time for last 1,000,000: 1s. Last read position: chr20:35,503,995
INFO 2026-05-28 00:09:20 MarkDuplicates Tracking 25570 as yet unmatched pairs. 4620 records in RAM.
INFO 2026-05-28 00:09:22 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 1s. Last read position: chr20:43,697,676
INFO 2026-05-28 00:09:22 MarkDuplicates Tracking 24160 as yet unmatched pairs. 3210 records in RAM.
INFO 2026-05-28 00:09:23 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 1s. Last read position: chr20:56,359,071
INFO 2026-05-28 00:09:23 MarkDuplicates Tracking 22977 as yet unmatched pairs. 2026 records in RAM.
INFO 2026-05-28 00:09:24 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:05:33s. Time for last 1,000,000: 1s. Last read position: chr21:8,214,657
INFO 2026-05-28 00:09:24 MarkDuplicates Tracking 20916 as yet unmatched pairs. 3604 records in RAM.
INFO 2026-05-28 00:09:26 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 1s. Last read position: chr21:36,057,132
INFO 2026-05-28 00:09:26 MarkDuplicates Tracking 19652 as yet unmatched pairs. 2338 records in RAM.
INFO 2026-05-28 00:09:27 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:05:36s. Time for last 1,000,000: 1s. Last read position: chr21:46,115,870
INFO 2026-05-28 00:09:27 MarkDuplicates Tracking 18769 as yet unmatched pairs. 1455 records in RAM.
INFO 2026-05-28 00:09:28 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:05:37s. Time for last 1,000,000: 1s. Last read position: chr22:24,119,488
INFO 2026-05-28 00:09:28 MarkDuplicates Tracking 16551 as yet unmatched pairs. 4416 records in RAM.
INFO 2026-05-28 00:09:30 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 1s. Last read position: chr22:36,300,911
INFO 2026-05-28 00:09:30 MarkDuplicates Tracking 15212 as yet unmatched pairs. 3077 records in RAM.
INFO 2026-05-28 00:09:32 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:05:41s. Time for last 1,000,000: 1s. Last read position: chr22:41,877,955
INFO 2026-05-28 00:09:32 MarkDuplicates Tracking 13482 as yet unmatched pairs. 1347 records in RAM.
INFO 2026-05-28 00:09:33 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 1s. Last read position: chrX:3,311,126
INFO 2026-05-28 00:09:33 MarkDuplicates Tracking 11801 as yet unmatched pairs. 10857 records in RAM.
INFO 2026-05-28 00:09:35 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 1s. Last read position: chrX:46,662,122
INFO 2026-05-28 00:09:35 MarkDuplicates Tracking 10258 as yet unmatched pairs. 9313 records in RAM.
INFO 2026-05-28 00:09:37 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chrX:53,627,852
INFO 2026-05-28 00:09:37 MarkDuplicates Tracking 8964 as yet unmatched pairs. 8019 records in RAM.
INFO 2026-05-28 00:09:39 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:05:48s. Time for last 1,000,000: 2s. Last read position: chrX:78,114,028
INFO 2026-05-28 00:09:39 MarkDuplicates Tracking 7774 as yet unmatched pairs. 6829 records in RAM.
INFO 2026-05-28 00:09:41 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 1s. Last read position: chrX:117,945,464
INFO 2026-05-28 00:09:41 MarkDuplicates Tracking 6271 as yet unmatched pairs. 5326 records in RAM.
INFO 2026-05-28 00:09:42 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 1s. Last read position: chrX:154,018,289
INFO 2026-05-28 00:09:42 MarkDuplicates Tracking 4824 as yet unmatched pairs. 3879 records in RAM.
INFO 2026-05-28 00:09:44 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 1s. Last read position: chrX:154,359,818
INFO 2026-05-28 00:09:44 MarkDuplicates Tracking 6229 as yet unmatched pairs. 5284 records in RAM.
INFO 2026-05-28 00:09:46 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:05:55s. Time for last 1,000,000: 1s. Last read position: chrX:154,367,690
INFO 2026-05-28 00:09:46 MarkDuplicates Tracking 5941 as yet unmatched pairs. 4996 records in RAM.
INFO 2026-05-28 00:09:47 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 1s. Last read position: KI270733.1:132,406
INFO 2026-05-28 00:09:47 MarkDuplicates Tracking 259 as yet unmatched pairs. 259 records in RAM.
INFO 2026-05-28 00:09:47 MarkDuplicates Read 208267718 records. 0 pairs never matched.
INFO 2026-05-28 00:09:56 MarkDuplicates After buildSortedReadEndLists freeMemory: 37064713504; totalMemory: 62042144768; maxMemory: 63585648640
INFO 2026-05-28 00:09:56 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-05-28 00:10:02 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-05-28 00:10:25 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-05-28 00:10:40 MarkDuplicates Sorting list of duplicate records.
INFO 2026-05-28 00:10:45 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300864656; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-05-28 00:10:45 MarkDuplicates Marking 111209482 records as duplicates.
INFO 2026-05-28 00:10:45 MarkDuplicates Found 6663737 optical duplicate clusters.
INFO 2026-05-28 00:10:45 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-05-28 00:11:06 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:21s. Time for last 10,000,000: 21s. Last read position: chr1:153,976,697
INFO 2026-05-28 00:11:30 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:45s. Time for last 10,000,000: 23s. Last read position: chr1:243,552,785
INFO 2026-05-28 00:11:54 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:09s. Time for last 10,000,000: 24s. Last read position: chr2:206,757,254
INFO 2026-05-28 00:12:18 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:33s. Time for last 10,000,000: 24s. Last read position: chr3:49,123,791
INFO 2026-05-28 00:12:43 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:58s. Time for last 10,000,000: 24s. Last read position: chr4:119,031,569
INFO 2026-05-28 00:13:07 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:22s. Time for last 10,000,000: 24s. Last read position: chr5:170,270,891
INFO 2026-05-28 00:13:31 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:46s. Time for last 10,000,000: 24s. Last read position: chr6:159,684,868
INFO 2026-05-28 00:13:54 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:09s. Time for last 10,000,000: 23s. Last read position: chr7:130,387,855
INFO 2026-05-28 00:14:19 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:34s. Time for last 10,000,000: 25s. Last read position: chr9:27,185,594
INFO 2026-05-28 00:14:43 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:58s. Time for last 10,000,000: 24s. Last read position: chr10:35,179,164
INFO 2026-05-28 00:15:08 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:04:22s. Time for last 10,000,000: 24s. Last read position: chr11:61,429,197
INFO 2026-05-28 00:15:28 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:04:43s. Time for last 10,000,000: 20s. Last read position: chr12:6,944,562
INFO 2026-05-28 00:15:50 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:05:05s. Time for last 10,000,000: 21s. Last read position: chr12:123,937,325
INFO 2026-05-28 00:16:11 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:05:26s. Time for last 10,000,000: 21s. Last read position: chr15:38,358,288
INFO 2026-05-28 00:16:33 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:05:48s. Time for last 10,000,000: 21s. Last read position: chr16:15,750,205
INFO 2026-05-28 00:16:54 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:06:09s. Time for last 10,000,000: 21s. Last read position: chr17:16,382,018
INFO 2026-05-28 00:17:17 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:06:32s. Time for last 10,000,000: 22s. Last read position: chr17:50,199,876
INFO 2026-05-28 00:17:41 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:06:56s. Time for last 10,000,000: 23s. Last read position: chr19:7,856,022
INFO 2026-05-28 00:18:03 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:07:18s. Time for last 10,000,000: 22s. Last read position: chr20:4,873,962
INFO 2026-05-28 00:18:24 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:07:39s. Time for last 10,000,000: 20s. Last read position: chrX:3,311,126
INFO 2026-05-28 00:18:42 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-05-28 00:18:42 MarkDuplicates Duplicate Index cleanup.
INFO 2026-05-28 00:18:42 MarkDuplicates Getting Memory Stats.
INFO 2026-05-28 00:18:42 MarkDuplicates Before output close freeMemory: 202273472; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-05-28 00:18:42 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-05-28 00:18:42 MarkDuplicates After output close freeMemory: 104336496; totalMemory: 134217728; maxMemory: 63585648640
[Thu May 28 00:18:42 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 14.89 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory