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/36/6f6202a1c2bee4019e4192cc380993/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/6f6202a1c2bee4019e4192cc380993/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/38f613398bb98d0c78bf28614199fa/659_b4x-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
==> 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_b4x-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bam --METRICS_FILE 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:33:10.114 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
[Mon Jun 08 07:33:10 GMT 2026] MarkDuplicates --INPUT 659_b4x-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_b4x-T1-TRNA-1_B23MHV2LT4_1.md.bam --METRICS_FILE 659_b4x-T1-TRNA-1_B23MHV2LT4_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
[Mon Jun 08 07:33:10 GMT 2026] Executing as ?@nf-366f6202a1c2bee4019e4192cc380993-53827-zx8j9 on Linux 6.12.88 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 2026-06-08 07:33:10 MarkDuplicates Start of doWork freeMemory: 105828000; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:33:10 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:33:10 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:33:15 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:8,362,744
INFO 2026-06-08 07:33:15 MarkDuplicates Tracking 1967 as yet unmatched pairs. 18 records in RAM.
INFO 2026-06-08 07:33:18 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 3s. Last read position: chr1:19,153,813
INFO 2026-06-08 07:33:18 MarkDuplicates Tracking 3610 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 07:33:21 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:09s. Time for last 1,000,000: 3s. Last read position: chr1:26,364,532
INFO 2026-06-08 07:33:21 MarkDuplicates Tracking 5274 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 07:33:24 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 2s. Last read position: chr1:33,276,583
INFO 2026-06-08 07:33:24 MarkDuplicates Tracking 7127 as yet unmatched pairs. 18 records in RAM.
INFO 2026-06-08 07:33:27 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:15s. Time for last 1,000,000: 2s. Last read position: chr1:43,653,158
INFO 2026-06-08 07:33:27 MarkDuplicates Tracking 8965 as yet unmatched pairs. 15 records in RAM.
INFO 2026-06-08 07:33:29 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: chr1:86,719,511
INFO 2026-06-08 07:33:29 MarkDuplicates Tracking 10553 as yet unmatched pairs. 15 records in RAM.
INFO 2026-06-08 07:33:32 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 2s. Last read position: chr1:116,390,324
INFO 2026-06-08 07:33:32 MarkDuplicates Tracking 12140 as yet unmatched pairs. 45 records in RAM.
INFO 2026-06-08 07:33:34 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr1:147,270,972
INFO 2026-06-08 07:33:34 MarkDuplicates Tracking 13347 as yet unmatched pairs. 13 records in RAM.
INFO 2026-06-08 07:33:36 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: chr1:151,307,600
INFO 2026-06-08 07:33:36 MarkDuplicates Tracking 14673 as yet unmatched pairs. 54 records in RAM.
INFO 2026-06-08 07:33:39 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 2s. Last read position: chr1:153,936,100
INFO 2026-06-08 07:33:39 MarkDuplicates Tracking 16056 as yet unmatched pairs. 78 records in RAM.
INFO 2026-06-08 07:33:41 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 2s. Last read position: chr1:155,765,888
INFO 2026-06-08 07:33:41 MarkDuplicates Tracking 17502 as yet unmatched pairs. 27 records in RAM.
INFO 2026-06-08 07:33:43 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 2s. Last read position: chr1:159,919,711
INFO 2026-06-08 07:33:43 MarkDuplicates Tracking 19296 as yet unmatched pairs. 8 records in RAM.
INFO 2026-06-08 07:33:46 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr1:178,473,102
INFO 2026-06-08 07:33:46 MarkDuplicates Tracking 20886 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:33:49 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:37s. Time for last 1,000,000: 2s. Last read position: chr1:201,982,707
INFO 2026-06-08 07:33:49 MarkDuplicates Tracking 22740 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:33:51 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:39s. Time for last 1,000,000: 2s. Last read position: chr1:225,517,647
INFO 2026-06-08 07:33:51 MarkDuplicates Tracking 24547 as yet unmatched pairs. 68 records in RAM.
INFO 2026-06-08 07:33:54 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr1:236,572,763
INFO 2026-06-08 07:33:54 MarkDuplicates Tracking 26437 as yet unmatched pairs. 25 records in RAM.
INFO 2026-06-08 07:33:56 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:44s. Time for last 1,000,000: 2s. Last read position: chr2:26,230,243
INFO 2026-06-08 07:33:56 MarkDuplicates Tracking 28295 as yet unmatched pairs. 28215 records in RAM.
INFO 2026-06-08 07:34:00 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 3s. Last read position: chr2:32,916,406
INFO 2026-06-08 07:34:00 MarkDuplicates Tracking 225157 as yet unmatched pairs. 12569 records in RAM.
INFO 2026-06-08 07:34:02 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr2:61,876,930
INFO 2026-06-08 07:34:02 MarkDuplicates Tracking 235088 as yet unmatched pairs. 10339 records in RAM.
INFO 2026-06-08 07:34:04 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr2:96,115,940
INFO 2026-06-08 07:34:04 MarkDuplicates Tracking 233598 as yet unmatched pairs. 8847 records in RAM.
INFO 2026-06-08 07:34:06 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr2:117,821,216
INFO 2026-06-08 07:34:06 MarkDuplicates Tracking 231938 as yet unmatched pairs. 7180 records in RAM.
INFO 2026-06-08 07:34:09 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:56s. Time for last 1,000,000: 2s. Last read position: chr2:174,571,910
INFO 2026-06-08 07:34:09 MarkDuplicates Tracking 230313 as yet unmatched pairs. 5546 records in RAM.
INFO 2026-06-08 07:34:11 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 2s. Last read position: chr2:205,763,794
INFO 2026-06-08 07:34:11 MarkDuplicates Tracking 228609 as yet unmatched pairs. 3838 records in RAM.
INFO 2026-06-08 07:34:13 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 2s. Last read position: chr2:222,201,269
INFO 2026-06-08 07:34:13 MarkDuplicates Tracking 227135 as yet unmatched pairs. 2361 records in RAM.
INFO 2026-06-08 07:34:15 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr2:237,525,758
INFO 2026-06-08 07:34:15 MarkDuplicates Tracking 225811 as yet unmatched pairs. 1018 records in RAM.
INFO 2026-06-08 07:34:17 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr3:12,836,169
INFO 2026-06-08 07:34:17 MarkDuplicates Tracking 223979 as yet unmatched pairs. 10371 records in RAM.
INFO 2026-06-08 07:34:20 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:08s. Time for last 1,000,000: 2s. Last read position: chr3:42,697,040
INFO 2026-06-08 07:34:20 MarkDuplicates Tracking 222608 as yet unmatched pairs. 8996 records in RAM.
INFO 2026-06-08 07:34:22 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 1s. Last read position: chr3:49,125,681
INFO 2026-06-08 07:34:22 MarkDuplicates Tracking 220315 as yet unmatched pairs. 6703 records in RAM.
INFO 2026-06-08 07:34:24 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:12s. Time for last 1,000,000: 1s. Last read position: chr3:69,965,065
INFO 2026-06-08 07:34:24 MarkDuplicates Tracking 219064 as yet unmatched pairs. 5448 records in RAM.
INFO 2026-06-08 07:34:25 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 1s. Last read position: chr3:127,015,202
INFO 2026-06-08 07:34:25 MarkDuplicates Tracking 217455 as yet unmatched pairs. 3833 records in RAM.
INFO 2026-06-08 07:34:27 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr3:170,391,234
INFO 2026-06-08 07:34:27 MarkDuplicates Tracking 215376 as yet unmatched pairs. 1751 records in RAM.
INFO 2026-06-08 07:34:29 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr3:196,661,136
INFO 2026-06-08 07:34:29 MarkDuplicates Tracking 213788 as yet unmatched pairs. 161 records in RAM.
INFO 2026-06-08 07:34:31 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr4:7,819,138
INFO 2026-06-08 07:34:31 MarkDuplicates Tracking 211955 as yet unmatched pairs. 4589 records in RAM.
INFO 2026-06-08 07:34:33 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 2s. Last read position: chr4:70,763,550
INFO 2026-06-08 07:34:33 MarkDuplicates Tracking 210159 as yet unmatched pairs. 2787 records in RAM.
INFO 2026-06-08 07:34:36 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 2s. Last read position: chr4:123,397,802
INFO 2026-06-08 07:34:36 MarkDuplicates Tracking 208509 as yet unmatched pairs. 1132 records in RAM.
INFO 2026-06-08 07:34:39 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:27s. Time for last 1,000,000: 3s. Last read position: chr5:14,280,336
INFO 2026-06-08 07:34:39 MarkDuplicates Tracking 206925 as yet unmatched pairs. 9619 records in RAM.
INFO 2026-06-08 07:34:42 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 2s. Last read position: chr5:56,880,708
INFO 2026-06-08 07:34:42 MarkDuplicates Tracking 205091 as yet unmatched pairs. 7783 records in RAM.
INFO 2026-06-08 07:34:44 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: chr5:119,175,298
INFO 2026-06-08 07:34:44 MarkDuplicates Tracking 203447 as yet unmatched pairs. 6135 records in RAM.
INFO 2026-06-08 07:34:47 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 2s. Last read position: chr5:139,682,944
INFO 2026-06-08 07:34:47 MarkDuplicates Tracking 201846 as yet unmatched pairs. 4532 records in RAM.
INFO 2026-06-08 07:34:50 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 3s. Last read position: chr5:150,405,130
INFO 2026-06-08 07:34:50 MarkDuplicates Tracking 200659 as yet unmatched pairs. 3273 records in RAM.
INFO 2026-06-08 07:34:52 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:40s. Time for last 1,000,000: 2s. Last read position: chr5:176,532,094
INFO 2026-06-08 07:34:52 MarkDuplicates Tracking 198600 as yet unmatched pairs. 1213 records in RAM.
INFO 2026-06-08 07:34:55 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 2s. Last read position: chr6:7,230,863
INFO 2026-06-08 07:34:55 MarkDuplicates Tracking 197186 as yet unmatched pairs. 10371 records in RAM.
INFO 2026-06-08 07:34:57 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr6:29,942,562
INFO 2026-06-08 07:34:57 MarkDuplicates Tracking 196053 as yet unmatched pairs. 9229 records in RAM.
INFO 2026-06-08 07:34:59 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: chr6:31,730,821
INFO 2026-06-08 07:34:59 MarkDuplicates Tracking 194061 as yet unmatched pairs. 7235 records in RAM.
INFO 2026-06-08 07:35:01 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 1s. Last read position: chr6:33,412,506
INFO 2026-06-08 07:35:01 MarkDuplicates Tracking 192296 as yet unmatched pairs. 5470 records in RAM.
INFO 2026-06-08 07:35:04 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: chr6:47,609,272
INFO 2026-06-08 07:35:04 MarkDuplicates Tracking 190775 as yet unmatched pairs. 3947 records in RAM.
INFO 2026-06-08 07:35:06 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: chr6:116,371,092
INFO 2026-06-08 07:35:06 MarkDuplicates Tracking 189160 as yet unmatched pairs. 2324 records in RAM.
INFO 2026-06-08 07:35:08 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 2s. Last read position: chr6:157,201,134
INFO 2026-06-08 07:35:08 MarkDuplicates Tracking 187608 as yet unmatched pairs. 768 records in RAM.
INFO 2026-06-08 07:35:10 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:58s. Time for last 1,000,000: 2s. Last read position: chr7:4,786,284
INFO 2026-06-08 07:35:10 MarkDuplicates Tracking 185877 as yet unmatched pairs. 17808 records in RAM.
INFO 2026-06-08 07:35:13 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr7:20,651,530
INFO 2026-06-08 07:35:13 MarkDuplicates Tracking 184071 as yet unmatched pairs. 16000 records in RAM.
INFO 2026-06-08 07:35:15 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: chr7:44,109,128
INFO 2026-06-08 07:35:15 MarkDuplicates Tracking 182591 as yet unmatched pairs. 14519 records in RAM.
INFO 2026-06-08 07:35:17 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr7:70,713,843
INFO 2026-06-08 07:35:17 MarkDuplicates Tracking 180832 as yet unmatched pairs. 12754 records in RAM.
INFO 2026-06-08 07:35:19 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 1s. Last read position: chr7:75,421,888
INFO 2026-06-08 07:35:19 MarkDuplicates Tracking 180006 as yet unmatched pairs. 11926 records in RAM.
INFO 2026-06-08 07:35:21 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 2s. Last read position: chr7:94,664,662
INFO 2026-06-08 07:35:21 MarkDuplicates Tracking 178477 as yet unmatched pairs. 10395 records in RAM.
INFO 2026-06-08 07:35:23 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 2s. Last read position: chr7:100,694,339
INFO 2026-06-08 07:35:23 MarkDuplicates Tracking 176780 as yet unmatched pairs. 8695 records in RAM.
INFO 2026-06-08 07:35:25 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 1s. Last read position: chr7:105,112,275
INFO 2026-06-08 07:35:25 MarkDuplicates Tracking 175684 as yet unmatched pairs. 7599 records in RAM.
INFO 2026-06-08 07:35:28 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 3s. Last read position: chr7:127,904,789
INFO 2026-06-08 07:35:28 MarkDuplicates Tracking 174123 as yet unmatched pairs. 6032 records in RAM.
INFO 2026-06-08 07:35:30 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr7:139,034,660
INFO 2026-06-08 07:35:30 MarkDuplicates Tracking 172074 as yet unmatched pairs. 3983 records in RAM.
INFO 2026-06-08 07:35:32 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 2s. Last read position: chr7:144,363,443
INFO 2026-06-08 07:35:32 MarkDuplicates Tracking 170512 as yet unmatched pairs. 2421 records in RAM.
INFO 2026-06-08 07:35:35 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 2s. Last read position: chr7:154,968,878
INFO 2026-06-08 07:35:35 MarkDuplicates Tracking 168754 as yet unmatched pairs. 662 records in RAM.
INFO 2026-06-08 07:35:37 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 2s. Last read position: chr8:18,765,449
INFO 2026-06-08 07:35:37 MarkDuplicates Tracking 166983 as yet unmatched pairs. 9698 records in RAM.
INFO 2026-06-08 07:35:39 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: chr8:37,697,833
INFO 2026-06-08 07:35:39 MarkDuplicates Tracking 165751 as yet unmatched pairs. 8462 records in RAM.
INFO 2026-06-08 07:35:41 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 2s. Last read position: chr8:58,572,205
INFO 2026-06-08 07:35:41 MarkDuplicates Tracking 163523 as yet unmatched pairs. 6230 records in RAM.
INFO 2026-06-08 07:35:43 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: chr8:100,721,460
INFO 2026-06-08 07:35:43 MarkDuplicates Tracking 162141 as yet unmatched pairs. 4845 records in RAM.
INFO 2026-06-08 07:35:45 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 2s. Last read position: chr8:138,877,986
INFO 2026-06-08 07:35:45 MarkDuplicates Tracking 160274 as yet unmatched pairs. 2973 records in RAM.
INFO 2026-06-08 07:35:48 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 3s. Last read position: chr8:144,083,852
INFO 2026-06-08 07:35:48 MarkDuplicates Tracking 158313 as yet unmatched pairs. 1003 records in RAM.
INFO 2026-06-08 07:35:51 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 2s. Last read position: chr9:12,702,336
INFO 2026-06-08 07:35:51 MarkDuplicates Tracking 156578 as yet unmatched pairs. 9858 records in RAM.
INFO 2026-06-08 07:35:53 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 2s. Last read position: chr9:66,918,629
INFO 2026-06-08 07:35:53 MarkDuplicates Tracking 154780 as yet unmatched pairs. 8038 records in RAM.
INFO 2026-06-08 07:35:56 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:44s. Time for last 1,000,000: 2s. Last read position: chr9:107,321,989
INFO 2026-06-08 07:35:56 MarkDuplicates Tracking 152917 as yet unmatched pairs. 6174 records in RAM.
INFO 2026-06-08 07:35:58 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:46s. Time for last 1,000,000: 2s. Last read position: chr9:127,818,174
INFO 2026-06-08 07:35:58 MarkDuplicates Tracking 151116 as yet unmatched pairs. 4371 records in RAM.
INFO 2026-06-08 07:36:01 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: chr9:131,588,922
INFO 2026-06-08 07:36:01 MarkDuplicates Tracking 149312 as yet unmatched pairs. 2566 records in RAM.
INFO 2026-06-08 07:36:04 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 2s. Last read position: chr9:137,014,986
INFO 2026-06-08 07:36:04 MarkDuplicates Tracking 147309 as yet unmatched pairs. 560 records in RAM.
INFO 2026-06-08 07:36:06 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 2s. Last read position: chr10:45,719,338
INFO 2026-06-08 07:36:06 MarkDuplicates Tracking 145569 as yet unmatched pairs. 3795 records in RAM.
INFO 2026-06-08 07:36:08 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 2s. Last read position: chr10:88,947,259
INFO 2026-06-08 07:36:08 MarkDuplicates Tracking 143855 as yet unmatched pairs. 2079 records in RAM.
INFO 2026-06-08 07:36:10 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 2s. Last read position: chr10:124,706,643
INFO 2026-06-08 07:36:10 MarkDuplicates Tracking 142049 as yet unmatched pairs. 261 records in RAM.
INFO 2026-06-08 07:36:13 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 2s. Last read position: chr11:2,390,503
INFO 2026-06-08 07:36:13 MarkDuplicates Tracking 140356 as yet unmatched pairs. 14338 records in RAM.
INFO 2026-06-08 07:36:15 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:03:03s. Time for last 1,000,000: 2s. Last read position: chr11:19,948,951
INFO 2026-06-08 07:36:15 MarkDuplicates Tracking 138675 as yet unmatched pairs. 12654 records in RAM.
INFO 2026-06-08 07:36:18 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: chr11:48,136,216
INFO 2026-06-08 07:36:18 MarkDuplicates Tracking 136876 as yet unmatched pairs. 10854 records in RAM.
INFO 2026-06-08 07:36:20 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 2s. Last read position: chr11:62,687,940
INFO 2026-06-08 07:36:20 MarkDuplicates Tracking 135148 as yet unmatched pairs. 9112 records in RAM.
INFO 2026-06-08 07:36:22 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:03:10s. Time for last 1,000,000: 2s. Last read position: chr11:65,581,751
INFO 2026-06-08 07:36:22 MarkDuplicates Tracking 132944 as yet unmatched pairs. 6906 records in RAM.
INFO 2026-06-08 07:36:25 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 2s. Last read position: chr11:67,401,174
INFO 2026-06-08 07:36:25 MarkDuplicates Tracking 130950 as yet unmatched pairs. 4912 records in RAM.
INFO 2026-06-08 07:36:27 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 2s. Last read position: chr11:75,441,677
INFO 2026-06-08 07:36:27 MarkDuplicates Tracking 129284 as yet unmatched pairs. 3242 records in RAM.
INFO 2026-06-08 07:36:30 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:18s. Time for last 1,000,000: 2s. Last read position: chr11:117,999,449
INFO 2026-06-08 07:36:30 MarkDuplicates Tracking 127779 as yet unmatched pairs. 1734 records in RAM.
INFO 2026-06-08 07:36:32 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 2s. Last read position: chr11:129,874,511
INFO 2026-06-08 07:36:32 MarkDuplicates Tracking 126198 as yet unmatched pairs. 150 records in RAM.
INFO 2026-06-08 07:36:34 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:22s. Time for last 1,000,000: 2s. Last read position: chr12:9,076,784
INFO 2026-06-08 07:36:34 MarkDuplicates Tracking 124615 as yet unmatched pairs. 12582 records in RAM.
INFO 2026-06-08 07:36:37 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:25s. Time for last 1,000,000: 2s. Last read position: chr12:49,029,428
INFO 2026-06-08 07:36:37 MarkDuplicates Tracking 122983 as yet unmatched pairs. 10947 records in RAM.
INFO 2026-06-08 07:36:39 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 2s. Last read position: chr12:53,062,408
INFO 2026-06-08 07:36:39 MarkDuplicates Tracking 121183 as yet unmatched pairs. 9145 records in RAM.
INFO 2026-06-08 07:36:41 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 2s. Last read position: chr12:56,252,836
INFO 2026-06-08 07:36:41 MarkDuplicates Tracking 119355 as yet unmatched pairs. 7316 records in RAM.
INFO 2026-06-08 07:36:44 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 2s. Last read position: chr12:62,566,380
INFO 2026-06-08 07:36:44 MarkDuplicates Tracking 117877 as yet unmatched pairs. 5837 records in RAM.
INFO 2026-06-08 07:36:46 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:34s. Time for last 1,000,000: 2s. Last read position: chr12:106,815,080
INFO 2026-06-08 07:36:46 MarkDuplicates Tracking 116016 as yet unmatched pairs. 3972 records in RAM.
INFO 2026-06-08 07:36:49 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:37s. Time for last 1,000,000: 2s. Last read position: chr12:121,175,406
INFO 2026-06-08 07:36:49 MarkDuplicates Tracking 114376 as yet unmatched pairs. 2331 records in RAM.
INFO 2026-06-08 07:36:52 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 2s. Last read position: chr12:131,961,579
INFO 2026-06-08 07:36:52 MarkDuplicates Tracking 112643 as yet unmatched pairs. 596 records in RAM.
INFO 2026-06-08 07:36:54 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 2s. Last read position: chr13:24,456,378
INFO 2026-06-08 07:36:54 MarkDuplicates Tracking 111053 as yet unmatched pairs. 6632 records in RAM.
INFO 2026-06-08 07:36:57 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:44s. Time for last 1,000,000: 2s. Last read position: chr13:43,970,676
INFO 2026-06-08 07:36:57 MarkDuplicates Tracking 109176 as yet unmatched pairs. 4753 records in RAM.
INFO 2026-06-08 07:36:59 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 2s. Last read position: chr13:79,405,793
INFO 2026-06-08 07:36:59 MarkDuplicates Tracking 107471 as yet unmatched pairs. 3046 records in RAM.
INFO 2026-06-08 07:37:01 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 2s. Last read position: chr13:108,270,115
INFO 2026-06-08 07:37:01 MarkDuplicates Tracking 105566 as yet unmatched pairs. 1139 records in RAM.
INFO 2026-06-08 07:37:03 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 2s. Last read position: chr14:23,026,217
INFO 2026-06-08 07:37:03 MarkDuplicates Tracking 103756 as yet unmatched pairs. 7413 records in RAM.
INFO 2026-06-08 07:37:05 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:53s. Time for last 1,000,000: 2s. Last read position: chr14:50,935,117
INFO 2026-06-08 07:37:05 MarkDuplicates Tracking 102161 as yet unmatched pairs. 5815 records in RAM.
INFO 2026-06-08 07:37:08 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:56s. Time for last 1,000,000: 2s. Last read position: chr14:71,108,638
INFO 2026-06-08 07:37:08 MarkDuplicates Tracking 100339 as yet unmatched pairs. 3993 records in RAM.
INFO 2026-06-08 07:37:10 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 2s. Last read position: chr14:93,720,739
INFO 2026-06-08 07:37:10 MarkDuplicates Tracking 98509 as yet unmatched pairs. 2159 records in RAM.
INFO 2026-06-08 07:37:12 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:04:00s. Time for last 1,000,000: 1s. Last read position: chr14:105,248,963
INFO 2026-06-08 07:37:12 MarkDuplicates Tracking 96781 as yet unmatched pairs. 417 records in RAM.
INFO 2026-06-08 07:37:14 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: chr15:31,050,471
INFO 2026-06-08 07:37:14 MarkDuplicates Tracking 95528 as yet unmatched pairs. 8962 records in RAM.
INFO 2026-06-08 07:37:16 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:04:04s. Time for last 1,000,000: 2s. Last read position: chr15:41,870,266
INFO 2026-06-08 07:37:16 MarkDuplicates Tracking 93989 as yet unmatched pairs. 7419 records in RAM.
INFO 2026-06-08 07:37:18 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:04:06s. Time for last 1,000,000: 2s. Last read position: chr15:52,153,963
INFO 2026-06-08 07:37:18 MarkDuplicates Tracking 92344 as yet unmatched pairs. 5774 records in RAM.
INFO 2026-06-08 07:37:21 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:04:09s. Time for last 1,000,000: 2s. Last read position: chr15:68,214,313
INFO 2026-06-08 07:37:21 MarkDuplicates Tracking 90942 as yet unmatched pairs. 4370 records in RAM.
INFO 2026-06-08 07:37:23 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 2s. Last read position: chr15:75,675,927
INFO 2026-06-08 07:37:23 MarkDuplicates Tracking 89163 as yet unmatched pairs. 2589 records in RAM.
INFO 2026-06-08 07:37:27 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 3s. Last read position: chr15:88,899,405
INFO 2026-06-08 07:37:27 MarkDuplicates Tracking 87666 as yet unmatched pairs. 1089 records in RAM.
INFO 2026-06-08 07:37:29 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:04:17s. Time for last 1,000,000: 2s. Last read position: chr16:715,302
INFO 2026-06-08 07:37:29 MarkDuplicates Tracking 86161 as yet unmatched pairs. 12958 records in RAM.
INFO 2026-06-08 07:37:32 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:04:20s. Time for last 1,000,000: 2s. Last read position: chr16:2,759,032
INFO 2026-06-08 07:37:32 MarkDuplicates Tracking 84004 as yet unmatched pairs. 10801 records in RAM.
INFO 2026-06-08 07:37:34 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 2s. Last read position: chr16:11,763,457
INFO 2026-06-08 07:37:34 MarkDuplicates Tracking 82442 as yet unmatched pairs. 9239 records in RAM.
INFO 2026-06-08 07:37:36 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:04:24s. Time for last 1,000,000: 2s. Last read position: chr16:16,318,012
INFO 2026-06-08 07:37:36 MarkDuplicates Tracking 81875 as yet unmatched pairs. 8669 records in RAM.
INFO 2026-06-08 07:37:38 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:04:26s. Time for last 1,000,000: 2s. Last read position: chr16:18,351,204
INFO 2026-06-08 07:37:38 MarkDuplicates Tracking 81361 as yet unmatched pairs. 8155 records in RAM.
INFO 2026-06-08 07:37:40 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:04:28s. Time for last 1,000,000: 1s. Last read position: chr16:21,411,114
INFO 2026-06-08 07:37:40 MarkDuplicates Tracking 80520 as yet unmatched pairs. 7314 records in RAM.
INFO 2026-06-08 07:37:41 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 1s. Last read position: chr16:27,448,931
INFO 2026-06-08 07:37:41 MarkDuplicates Tracking 79784 as yet unmatched pairs. 6576 records in RAM.
INFO 2026-06-08 07:37:44 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:32s. Time for last 1,000,000: 2s. Last read position: chr16:29,834,010
INFO 2026-06-08 07:37:44 MarkDuplicates Tracking 78626 as yet unmatched pairs. 5417 records in RAM.
INFO 2026-06-08 07:37:46 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:34s. Time for last 1,000,000: 2s. Last read position: chr16:31,180,208
INFO 2026-06-08 07:37:46 MarkDuplicates Tracking 77484 as yet unmatched pairs. 4271 records in RAM.
INFO 2026-06-08 07:37:49 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 2s. Last read position: chr16:67,438,548
INFO 2026-06-08 07:37:49 MarkDuplicates Tracking 75702 as yet unmatched pairs. 2482 records in RAM.
INFO 2026-06-08 07:37:51 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:04:39s. Time for last 1,000,000: 2s. Last read position: chr16:88,429,003
INFO 2026-06-08 07:37:51 MarkDuplicates Tracking 74132 as yet unmatched pairs. 912 records in RAM.
INFO 2026-06-08 07:37:54 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:04:42s. Time for last 1,000,000: 2s. Last read position: chr17:2,376,894
INFO 2026-06-08 07:37:54 MarkDuplicates Tracking 72368 as yet unmatched pairs. 17762 records in RAM.
INFO 2026-06-08 07:37:57 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 2s. Last read position: chr17:7,557,454
INFO 2026-06-08 07:37:57 MarkDuplicates Tracking 70696 as yet unmatched pairs. 16089 records in RAM.
INFO 2026-06-08 07:37:59 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:04:47s. Time for last 1,000,000: 2s. Last read position: chr17:18,333,246
INFO 2026-06-08 07:37:59 MarkDuplicates Tracking 68848 as yet unmatched pairs. 14239 records in RAM.
INFO 2026-06-08 07:38:01 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 2s. Last read position: chr17:35,363,505
INFO 2026-06-08 07:38:01 MarkDuplicates Tracking 67119 as yet unmatched pairs. 12510 records in RAM.
INFO 2026-06-08 07:38:03 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:04:51s. Time for last 1,000,000: 2s. Last read position: chr17:40,262,604
INFO 2026-06-08 07:38:03 MarkDuplicates Tracking 65673 as yet unmatched pairs. 11064 records in RAM.
INFO 2026-06-08 07:38:05 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:04:53s. Time for last 1,000,000: 2s. Last read position: chr17:45,518,906
INFO 2026-06-08 07:38:05 MarkDuplicates Tracking 63843 as yet unmatched pairs. 9233 records in RAM.
INFO 2026-06-08 07:38:08 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:04:56s. Time for last 1,000,000: 2s. Last read position: chr17:50,199,252
INFO 2026-06-08 07:38:08 MarkDuplicates Tracking 62151 as yet unmatched pairs. 7541 records in RAM.
INFO 2026-06-08 07:38:11 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 2s. Last read position: chr17:63,810,537
INFO 2026-06-08 07:38:11 MarkDuplicates Tracking 60385 as yet unmatched pairs. 5772 records in RAM.
INFO 2026-06-08 07:38:13 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:05:01s. Time for last 1,000,000: 2s. Last read position: chr17:76,101,737
INFO 2026-06-08 07:38:13 MarkDuplicates Tracking 58674 as yet unmatched pairs. 4057 records in RAM.
INFO 2026-06-08 07:38:15 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 2s. Last read position: chr17:80,352,947
INFO 2026-06-08 07:38:15 MarkDuplicates Tracking 57046 as yet unmatched pairs. 2429 records in RAM.
INFO 2026-06-08 07:38:17 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:05:05s. Time for last 1,000,000: 2s. Last read position: chr17:82,238,780
INFO 2026-06-08 07:38:17 MarkDuplicates Tracking 54951 as yet unmatched pairs. 333 records in RAM.
INFO 2026-06-08 07:38:19 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 2s. Last read position: chr18:49,843,273
INFO 2026-06-08 07:38:19 MarkDuplicates Tracking 53328 as yet unmatched pairs. 1321 records in RAM.
INFO 2026-06-08 07:38:22 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 2s. Last read position: chr19:1,013,289
INFO 2026-06-08 07:38:22 MarkDuplicates Tracking 51674 as yet unmatched pairs. 21849 records in RAM.
INFO 2026-06-08 07:38:25 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 2s. Last read position: chr19:3,381,957
INFO 2026-06-08 07:38:25 MarkDuplicates Tracking 49680 as yet unmatched pairs. 19853 records in RAM.
INFO 2026-06-08 07:38:27 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:05:15s. Time for last 1,000,000: 2s. Last read position: chr19:8,241,407
INFO 2026-06-08 07:38:27 MarkDuplicates Tracking 47710 as yet unmatched pairs. 17883 records in RAM.
INFO 2026-06-08 07:38:29 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 2s. Last read position: chr19:12,657,537
INFO 2026-06-08 07:38:29 MarkDuplicates Tracking 45895 as yet unmatched pairs. 16068 records in RAM.
INFO 2026-06-08 07:38:32 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 2s. Last read position: chr19:15,255,568
INFO 2026-06-08 07:38:32 MarkDuplicates Tracking 43727 as yet unmatched pairs. 13900 records in RAM.
INFO 2026-06-08 07:38:34 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:05:22s. Time for last 1,000,000: 2s. Last read position: chr19:18,539,596
INFO 2026-06-08 07:38:34 MarkDuplicates Tracking 41690 as yet unmatched pairs. 11856 records in RAM.
INFO 2026-06-08 07:38:36 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:05:24s. Time for last 1,000,000: 2s. Last read position: chr19:35,721,015
INFO 2026-06-08 07:38:36 MarkDuplicates Tracking 39815 as yet unmatched pairs. 9980 records in RAM.
INFO 2026-06-08 07:38:38 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:05:26s. Time for last 1,000,000: 2s. Last read position: chr19:41,304,112
INFO 2026-06-08 07:38:38 MarkDuplicates Tracking 38007 as yet unmatched pairs. 8171 records in RAM.
INFO 2026-06-08 07:38:40 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:05:28s. Time for last 1,000,000: 2s. Last read position: chr19:42,326,265
INFO 2026-06-08 07:38:40 MarkDuplicates Tracking 36118 as yet unmatched pairs. 6282 records in RAM.
INFO 2026-06-08 07:38:42 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:05:30s. Time for last 1,000,000: 2s. Last read position: chr19:47,701,946
INFO 2026-06-08 07:38:42 MarkDuplicates Tracking 33903 as yet unmatched pairs. 4060 records in RAM.
INFO 2026-06-08 07:38:44 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:05:32s. Time for last 1,000,000: 2s. Last read position: chr19:49,888,201
INFO 2026-06-08 07:38:44 MarkDuplicates Tracking 32100 as yet unmatched pairs. 2256 records in RAM.
INFO 2026-06-08 07:38:47 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 2s. Last read position: chr19:57,320,770
INFO 2026-06-08 07:38:47 MarkDuplicates Tracking 30321 as yet unmatched pairs. 476 records in RAM.
INFO 2026-06-08 07:38:50 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:05:38s. Time for last 1,000,000: 2s. Last read position: chr20:25,259,317
INFO 2026-06-08 07:38:50 MarkDuplicates Tracking 28480 as yet unmatched pairs. 4288 records in RAM.
INFO 2026-06-08 07:38:52 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:05:40s. Time for last 1,000,000: 2s. Last read position: chr20:45,416,199
INFO 2026-06-08 07:38:52 MarkDuplicates Tracking 26681 as yet unmatched pairs. 2486 records in RAM.
INFO 2026-06-08 07:38:54 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:05:42s. Time for last 1,000,000: 2s. Last read position: chr20:62,914,295
INFO 2026-06-08 07:38:54 MarkDuplicates Tracking 24964 as yet unmatched pairs. 766 records in RAM.
INFO 2026-06-08 07:38:56 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:05:44s. Time for last 1,000,000: 2s. Last read position: chr21:8,216,192
INFO 2026-06-08 07:38:56 MarkDuplicates Tracking 23542 as yet unmatched pairs. 4283 records in RAM.
INFO 2026-06-08 07:38:58 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:05:46s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,739
INFO 2026-06-08 07:38:58 MarkDuplicates Tracking 23162 as yet unmatched pairs. 3900 records in RAM.
INFO 2026-06-08 07:38:59 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,985
INFO 2026-06-08 07:38:59 MarkDuplicates Tracking 22387 as yet unmatched pairs. 3116 records in RAM.
INFO 2026-06-08 07:39:01 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:05:49s. Time for last 1,000,000: 1s. Last read position: chr21:33,588,232
INFO 2026-06-08 07:39:01 MarkDuplicates Tracking 21000 as yet unmatched pairs. 1728 records in RAM.
INFO 2026-06-08 07:39:03 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:05:51s. Time for last 1,000,000: 2s. Last read position: chr22:11,251,040
INFO 2026-06-08 07:39:03 MarkDuplicates Tracking 19274 as yet unmatched pairs. 8300 records in RAM.
INFO 2026-06-08 07:39:06 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:05:54s. Time for last 1,000,000: 2s. Last read position: chr22:24,041,263
INFO 2026-06-08 07:39:06 MarkDuplicates Tracking 17701 as yet unmatched pairs. 6727 records in RAM.
INFO 2026-06-08 07:39:08 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:05:56s. Time for last 1,000,000: 2s. Last read position: chr22:35,781,611
INFO 2026-06-08 07:39:08 MarkDuplicates Tracking 15839 as yet unmatched pairs. 4865 records in RAM.
INFO 2026-06-08 07:39:10 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:05:58s. Time for last 1,000,000: 1s. Last read position: chr22:38,739,356
INFO 2026-06-08 07:39:10 MarkDuplicates Tracking 13801 as yet unmatched pairs. 2827 records in RAM.
INFO 2026-06-08 07:39:12 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 2s. Last read position: chr22:50,278,215
INFO 2026-06-08 07:39:12 MarkDuplicates Tracking 11932 as yet unmatched pairs. 958 records in RAM.
INFO 2026-06-08 07:39:15 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:06:03s. Time for last 1,000,000: 2s. Last read position: chrX:24,068,021
INFO 2026-06-08 07:39:15 MarkDuplicates Tracking 10090 as yet unmatched pairs. 4701 records in RAM.
INFO 2026-06-08 07:39:17 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:06:05s. Time for last 1,000,000: 2s. Last read position: chrX:54,810,034
INFO 2026-06-08 07:39:17 MarkDuplicates Tracking 8635 as yet unmatched pairs. 3244 records in RAM.
INFO 2026-06-08 07:39:20 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 2s. Last read position: chrX:130,015,042
INFO 2026-06-08 07:39:20 MarkDuplicates Tracking 7033 as yet unmatched pairs. 1639 records in RAM.
INFO 2026-06-08 07:39:22 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:06:10s. Time for last 1,000,000: 2s. Last read position: chrX:155,458,038
INFO 2026-06-08 07:39:22 MarkDuplicates Tracking 5407 as yet unmatched pairs. 12 records in RAM.
INFO 2026-06-08 07:39:24 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:06:12s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,727
INFO 2026-06-08 07:39:24 MarkDuplicates Tracking 3873 as yet unmatched pairs. 141 records in RAM.
INFO 2026-06-08 07:39:25 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:06:13s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,715
INFO 2026-06-08 07:39:25 MarkDuplicates Tracking 3734 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 07:39:27 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:06:15s. Time for last 1,000,000: 1s. Last read position: KI270733.1:133,624
INFO 2026-06-08 07:39:27 MarkDuplicates Tracking 452 as yet unmatched pairs. 438 records in RAM.
INFO 2026-06-08 07:39:28 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:06:16s. Time for last 1,000,000: 1s. Last read position: KI270733.1:178,719
INFO 2026-06-08 07:39:28 MarkDuplicates Tracking 16 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 07:39:28 MarkDuplicates Read 162116892 records. 0 pairs never matched.
INFO 2026-06-08 07:39:37 MarkDuplicates After buildSortedReadEndLists freeMemory: 41945220480; totalMemory: 61069066240; maxMemory: 63585648640
INFO 2026-06-08 07:39:37 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:39:43 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:40:21 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:40:39 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:40:44 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300860280; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-06-08 07:40:44 MarkDuplicates Marking 121567627 records as duplicates.
INFO 2026-06-08 07:40:44 MarkDuplicates Found 1364272 optical duplicate clusters.
INFO 2026-06-08 07:40:44 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:41:10 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:25s. Time for last 10,000,000: 25s. Last read position: chr1:153,936,100
INFO 2026-06-08 07:41:34 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:49s. Time for last 10,000,000: 23s. Last read position: chr2:96,115,940
INFO 2026-06-08 07:41:57 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:12s. Time for last 10,000,000: 23s. Last read position: chr3:127,015,202
INFO 2026-06-08 07:42:20 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:36s. Time for last 10,000,000: 23s. Last read position: chr5:150,405,130
INFO 2026-06-08 07:42:42 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:57s. Time for last 10,000,000: 21s. Last read position: chr7:20,651,530
INFO 2026-06-08 07:43:05 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:20s. Time for last 10,000,000: 22s. Last read position: chr7:154,968,878
INFO 2026-06-08 07:43:27 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:42s. Time for last 10,000,000: 22s. Last read position: chr9:127,818,174
INFO 2026-06-08 07:43:49 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:05s. Time for last 10,000,000: 22s. Last read position: chr11:65,581,751
INFO 2026-06-08 07:44:12 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:03:27s. Time for last 10,000,000: 22s. Last read position: chr12:106,815,080
INFO 2026-06-08 07:44:34 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:49s. Time for last 10,000,000: 22s. Last read position: chr14:93,720,739
INFO 2026-06-08 07:44:58 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:04:13s. Time for last 10,000,000: 23s. Last read position: chr16:11,763,457
INFO 2026-06-08 07:45:20 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:04:35s. Time for last 10,000,000: 22s. Last read position: chr17:7,557,454
INFO 2026-06-08 07:45:43 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:04:58s. Time for last 10,000,000: 22s. Last read position: chr18:49,843,273
INFO 2026-06-08 07:46:05 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:05:20s. Time for last 10,000,000: 22s. Last read position: chr19:47,701,946
INFO 2026-06-08 07:46:28 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:05:43s. Time for last 10,000,000: 22s. Last read position: chr22:11,251,040
INFO 2026-06-08 07:46:50 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:06:05s. Time for last 10,000,000: 22s. Last read position: GL000220.1:160,715
INFO 2026-06-08 07:46:58 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:46:58 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:46:58 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:46:58 MarkDuplicates Before output close freeMemory: 201694648; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 07:46:58 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:46:59 MarkDuplicates After output close freeMemory: 104325984; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 07:46:59 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 13.82 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory