Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/3e98ebb2e106bde6b4b95a0efca3ef/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/3e98ebb2e106bde6b4b95a0efca3ef/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/630599d91bbcb25f0d0e1ec8d306f0/659_ciZ-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-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_ciZ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bam --METRICS_FILE 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
00:00:45.408 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 00:00:45 GMT 2026] MarkDuplicates --INPUT 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT 659_ciZ-T1-TRNA-1_B23WHTKLT4_1.md.bam --METRICS_FILE 659_ciZ-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 00:00:45 GMT 2026] Executing as ?@nf-893e98ebb2e106bde6b4b95a0efca3ef-a0df8-8cn45 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 00:00:45 MarkDuplicates Start of doWork freeMemory: 105829920; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-05-28 00:00:45 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-05-28 00:00:45 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-05-28 00:00:53 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 5s. Last read position: chr1:6,349,844
INFO 2026-05-28 00:00:53 MarkDuplicates Tracking 1546 as yet unmatched pairs. 12 records in RAM.
INFO 2026-05-28 00:00:56 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 3s. Last read position: chr1:15,725,420
INFO 2026-05-28 00:00:56 MarkDuplicates Tracking 3000 as yet unmatched pairs. 16 records in RAM.
INFO 2026-05-28 00:01:01 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 5s. Last read position: chr1:21,823,209
INFO 2026-05-28 00:01:01 MarkDuplicates Tracking 4409 as yet unmatched pairs. 106 records in RAM.
INFO 2026-05-28 00:01:06 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 4s. Last read position: chr1:25,554,000
INFO 2026-05-28 00:01:06 MarkDuplicates Tracking 5675 as yet unmatched pairs. 37 records in RAM.
INFO 2026-05-28 00:01:09 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 3s. Last read position: chr1:31,584,862
INFO 2026-05-28 00:01:09 MarkDuplicates Tracking 7303 as yet unmatched pairs. 212 records in RAM.
INFO 2026-05-28 00:01:14 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 4s. Last read position: chr1:37,483,430
INFO 2026-05-28 00:01:14 MarkDuplicates Tracking 8706 as yet unmatched pairs. 210 records in RAM.
INFO 2026-05-28 00:01:18 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 4s. Last read position: chr1:43,620,980
INFO 2026-05-28 00:01:18 MarkDuplicates Tracking 9940 as yet unmatched pairs. 141 records in RAM.
INFO 2026-05-28 00:01:22 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 3s. Last read position: chr1:53,258,338
INFO 2026-05-28 00:01:22 MarkDuplicates Tracking 11144 as yet unmatched pairs. 16 records in RAM.
INFO 2026-05-28 00:01:26 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 4s. Last read position: chr1:85,582,451
INFO 2026-05-28 00:01:26 MarkDuplicates Tracking 12483 as yet unmatched pairs. 62 records in RAM.
INFO 2026-05-28 00:01:30 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 4s. Last read position: chr1:110,017,962
INFO 2026-05-28 00:01:30 MarkDuplicates Tracking 13674 as yet unmatched pairs. 53 records in RAM.
INFO 2026-05-28 00:01:34 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 4s. Last read position: chr1:117,442,267
INFO 2026-05-28 00:01:34 MarkDuplicates Tracking 14929 as yet unmatched pairs. 33 records in RAM.
INFO 2026-05-28 00:01:38 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 3s. Last read position: chr1:148,549,603
INFO 2026-05-28 00:01:38 MarkDuplicates Tracking 15953 as yet unmatched pairs. 79 records in RAM.
INFO 2026-05-28 00:01:41 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:53s. Time for last 1,000,000: 3s. Last read position: chr1:151,405,771
INFO 2026-05-28 00:01:41 MarkDuplicates Tracking 16918 as yet unmatched pairs. 39 records in RAM.
INFO 2026-05-28 00:01:46 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:58s. Time for last 1,000,000: 4s. Last read position: chr1:155,140,037
INFO 2026-05-28 00:01:46 MarkDuplicates Tracking 18346 as yet unmatched pairs. 192 records in RAM.
INFO 2026-05-28 00:01:50 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 3s. Last read position: chr1:156,677,032
INFO 2026-05-28 00:01:50 MarkDuplicates Tracking 19454 as yet unmatched pairs. 4 records in RAM.
INFO 2026-05-28 00:01:53 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 3s. Last read position: chr1:169,127,276
INFO 2026-05-28 00:01:53 MarkDuplicates Tracking 21149 as yet unmatched pairs. 355 records in RAM.
INFO 2026-05-28 00:01:58 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:01:10s. Time for last 1,000,000: 4s. Last read position: chr1:183,630,573
INFO 2026-05-28 00:01:58 MarkDuplicates Tracking 22234 as yet unmatched pairs. 177 records in RAM.
INFO 2026-05-28 00:02:02 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 4s. Last read position: chr1:203,698,239
INFO 2026-05-28 00:02:02 MarkDuplicates Tracking 23366 as yet unmatched pairs. 28 records in RAM.
INFO 2026-05-28 00:02:05 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 3s. Last read position: chr1:207,785,075
INFO 2026-05-28 00:02:05 MarkDuplicates Tracking 24981 as yet unmatched pairs. 406 records in RAM.
INFO 2026-05-28 00:02:09 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:01:21s. Time for last 1,000,000: 4s. Last read position: chr1:226,392,223
INFO 2026-05-28 00:02:09 MarkDuplicates Tracking 25766 as yet unmatched pairs. 21 records in RAM.
INFO 2026-05-28 00:02:13 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:01:25s. Time for last 1,000,000: 3s. Last read position: chr1:244,859,275
INFO 2026-05-28 00:02:13 MarkDuplicates Tracking 27374 as yet unmatched pairs. 270 records in RAM.
INFO 2026-05-28 00:02:17 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 4s. Last read position: chr2:24,691,544
INFO 2026-05-28 00:02:17 MarkDuplicates Tracking 28462 as yet unmatched pairs. 28424 records in RAM.
INFO 2026-05-28 00:02:21 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 4s. Last read position: chr2:32,916,256
INFO 2026-05-28 00:02:21 MarkDuplicates Tracking 41996 as yet unmatched pairs. 28756 records in RAM.
INFO 2026-05-28 00:02:25 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 4s. Last read position: chr2:38,564,552
INFO 2026-05-28 00:02:25 MarkDuplicates Tracking 247443 as yet unmatched pairs. 18088 records in RAM.
INFO 2026-05-28 00:02:29 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 3s. Last read position: chr2:54,626,191
INFO 2026-05-28 00:02:29 MarkDuplicates Tracking 246012 as yet unmatched pairs. 16657 records in RAM.
INFO 2026-05-28 00:02:32 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 3s. Last read position: chr2:65,332,040
INFO 2026-05-28 00:02:32 MarkDuplicates Tracking 244683 as yet unmatched pairs. 15326 records in RAM.
INFO 2026-05-28 00:02:36 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:48s. Time for last 1,000,000: 3s. Last read position: chr2:85,394,809
INFO 2026-05-28 00:02:36 MarkDuplicates Tracking 243485 as yet unmatched pairs. 14126 records in RAM.
INFO 2026-05-28 00:02:40 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 4s. Last read position: chr2:101,059,526
INFO 2026-05-28 00:02:40 MarkDuplicates Tracking 242197 as yet unmatched pairs. 12838 records in RAM.
INFO 2026-05-28 00:02:44 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:56s. Time for last 1,000,000: 3s. Last read position: chr2:113,227,227
INFO 2026-05-28 00:02:44 MarkDuplicates Tracking 241185 as yet unmatched pairs. 11826 records in RAM.
INFO 2026-05-28 00:02:48 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:02:00s. Time for last 1,000,000: 3s. Last read position: chr2:156,327,881
INFO 2026-05-28 00:02:48 MarkDuplicates Tracking 239938 as yet unmatched pairs. 10575 records in RAM.
INFO 2026-05-28 00:02:52 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 4s. Last read position: chr2:174,229,387
INFO 2026-05-28 00:02:52 MarkDuplicates Tracking 238994 as yet unmatched pairs. 9626 records in RAM.
INFO 2026-05-28 00:02:55 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 3s. Last read position: chr2:188,993,374
INFO 2026-05-28 00:02:55 MarkDuplicates Tracking 237606 as yet unmatched pairs. 8233 records in RAM.
INFO 2026-05-28 00:02:59 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 3s. Last read position: chr2:197,494,221
INFO 2026-05-28 00:02:59 MarkDuplicates Tracking 236814 as yet unmatched pairs. 7439 records in RAM.
INFO 2026-05-28 00:03:03 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 4s. Last read position: chr2:208,248,490
INFO 2026-05-28 00:03:03 MarkDuplicates Tracking 235168 as yet unmatched pairs. 5790 records in RAM.
INFO 2026-05-28 00:03:07 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 3s. Last read position: chr2:218,277,009
INFO 2026-05-28 00:03:07 MarkDuplicates Tracking 234748 as yet unmatched pairs. 5370 records in RAM.
INFO 2026-05-28 00:03:10 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 3s. Last read position: chr2:224,500,361
INFO 2026-05-28 00:03:10 MarkDuplicates Tracking 232435 as yet unmatched pairs. 3053 records in RAM.
INFO 2026-05-28 00:03:15 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 4s. Last read position: chr2:233,841,059
INFO 2026-05-28 00:03:15 MarkDuplicates Tracking 231128 as yet unmatched pairs. 1746 records in RAM.
INFO 2026-05-28 00:03:19 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 4s. Last read position: chr2:241,343,760
INFO 2026-05-28 00:03:19 MarkDuplicates Tracking 229733 as yet unmatched pairs. 351 records in RAM.
INFO 2026-05-28 00:03:23 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 4s. Last read position: chr3:23,889,112
INFO 2026-05-28 00:03:23 MarkDuplicates Tracking 228240 as yet unmatched pairs. 11823 records in RAM.
INFO 2026-05-28 00:03:26 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 3s. Last read position: chr3:42,194,855
INFO 2026-05-28 00:03:26 MarkDuplicates Tracking 226865 as yet unmatched pairs. 10445 records in RAM.
INFO 2026-05-28 00:03:31 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 4s. Last read position: chr3:48,599,634
INFO 2026-05-28 00:03:31 MarkDuplicates Tracking 225617 as yet unmatched pairs. 9197 records in RAM.
INFO 2026-05-28 00:03:35 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 3s. Last read position: chr3:51,703,976
INFO 2026-05-28 00:03:35 MarkDuplicates Tracking 224010 as yet unmatched pairs. 7589 records in RAM.
INFO 2026-05-28 00:03:38 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:02:50s. Time for last 1,000,000: 3s. Last read position: chr3:58,169,780
INFO 2026-05-28 00:03:38 MarkDuplicates Tracking 222710 as yet unmatched pairs. 6282 records in RAM.
INFO 2026-05-28 00:03:42 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 3s. Last read position: chr3:113,788,750
INFO 2026-05-28 00:03:42 MarkDuplicates Tracking 221376 as yet unmatched pairs. 4946 records in RAM.
INFO 2026-05-28 00:03:46 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:02:58s. Time for last 1,000,000: 3s. Last read position: chr3:129,272,822
INFO 2026-05-28 00:03:46 MarkDuplicates Tracking 220015 as yet unmatched pairs. 3584 records in RAM.
INFO 2026-05-28 00:03:49 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:03:01s. Time for last 1,000,000: 3s. Last read position: chr3:158,646,163
INFO 2026-05-28 00:03:49 MarkDuplicates Tracking 218718 as yet unmatched pairs. 2286 records in RAM.
INFO 2026-05-28 00:03:53 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:03:05s. Time for last 1,000,000: 3s. Last read position: chr3:185,417,738
INFO 2026-05-28 00:03:53 MarkDuplicates Tracking 217574 as yet unmatched pairs. 1142 records in RAM.
INFO 2026-05-28 00:03:56 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 3s. Last read position: chr3:197,696,982
INFO 2026-05-28 00:03:56 MarkDuplicates Tracking 216512 as yet unmatched pairs. 80 records in RAM.
INFO 2026-05-28 00:04:00 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:03:12s. Time for last 1,000,000: 3s. Last read position: chr4:6,863,361
INFO 2026-05-28 00:04:00 MarkDuplicates Tracking 215088 as yet unmatched pairs. 6642 records in RAM.
INFO 2026-05-28 00:04:03 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:03:16s. Time for last 1,000,000: 3s. Last read position: chr4:39,917,125
INFO 2026-05-28 00:04:03 MarkDuplicates Tracking 213901 as yet unmatched pairs. 5455 records in RAM.
INFO 2026-05-28 00:04:08 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:03:20s. Time for last 1,000,000: 4s. Last read position: chr4:75,936,112
INFO 2026-05-28 00:04:08 MarkDuplicates Tracking 212500 as yet unmatched pairs. 4052 records in RAM.
INFO 2026-05-28 00:04:11 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 3s. Last read position: chr4:102,613,432
INFO 2026-05-28 00:04:11 MarkDuplicates Tracking 211180 as yet unmatched pairs. 2730 records in RAM.
INFO 2026-05-28 00:04:15 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 3s. Last read position: chr4:143,545,471
INFO 2026-05-28 00:04:15 MarkDuplicates Tracking 209923 as yet unmatched pairs. 1473 records in RAM.
INFO 2026-05-28 00:04:19 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:03:31s. Time for last 1,000,000: 3s. Last read position: chr4:185,657,450
INFO 2026-05-28 00:04:19 MarkDuplicates Tracking 208770 as yet unmatched pairs. 319 records in RAM.
INFO 2026-05-28 00:04:23 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 3s. Last read position: chr5:17,354,187
INFO 2026-05-28 00:04:23 MarkDuplicates Tracking 207447 as yet unmatched pairs. 9956 records in RAM.
INFO 2026-05-28 00:04:27 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:03:39s. Time for last 1,000,000: 4s. Last read position: chr5:65,224,986
INFO 2026-05-28 00:04:27 MarkDuplicates Tracking 206267 as yet unmatched pairs. 8776 records in RAM.
INFO 2026-05-28 00:04:31 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:03:43s. Time for last 1,000,000: 3s. Last read position: chr5:83,204,858
INFO 2026-05-28 00:04:31 MarkDuplicates Tracking 205155 as yet unmatched pairs. 7661 records in RAM.
INFO 2026-05-28 00:04:35 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 4s. Last read position: chr5:132,210,511
INFO 2026-05-28 00:04:35 MarkDuplicates Tracking 203905 as yet unmatched pairs. 6410 records in RAM.
INFO 2026-05-28 00:04:39 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 3s. Last read position: chr5:140,632,343
INFO 2026-05-28 00:04:39 MarkDuplicates Tracking 202645 as yet unmatched pairs. 5142 records in RAM.
INFO 2026-05-28 00:04:43 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 3s. Last read position: chr5:150,402,582
INFO 2026-05-28 00:04:43 MarkDuplicates Tracking 203837 as yet unmatched pairs. 6324 records in RAM.
INFO 2026-05-28 00:04:46 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:03:58s. Time for last 1,000,000: 3s. Last read position: chr5:168,431,318
INFO 2026-05-28 00:04:46 MarkDuplicates Tracking 200215 as yet unmatched pairs. 2699 records in RAM.
INFO 2026-05-28 00:04:51 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:04:03s. Time for last 1,000,000: 4s. Last read position: chr5:177,882,652
INFO 2026-05-28 00:04:51 MarkDuplicates Tracking 198957 as yet unmatched pairs. 1440 records in RAM.
INFO 2026-05-28 00:04:55 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:04:07s. Time for last 1,000,000: 3s. Last read position: chr5:181,238,161
INFO 2026-05-28 00:04:55 MarkDuplicates Tracking 198477 as yet unmatched pairs. 958 records in RAM.
INFO 2026-05-28 00:04:59 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:04:11s. Time for last 1,000,000: 3s. Last read position: chr6:17,764,355
INFO 2026-05-28 00:04:59 MarkDuplicates Tracking 196406 as yet unmatched pairs. 13144 records in RAM.
INFO 2026-05-28 00:05:03 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:04:15s. Time for last 1,000,000: 3s. Last read position: chr6:29,942,814
INFO 2026-05-28 00:05:03 MarkDuplicates Tracking 195913 as yet unmatched pairs. 12650 records in RAM.
INFO 2026-05-28 00:05:06 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:04:18s. Time for last 1,000,000: 3s. Last read position: chr6:31,635,444
INFO 2026-05-28 00:05:06 MarkDuplicates Tracking 193759 as yet unmatched pairs. 10496 records in RAM.
INFO 2026-05-28 00:05:10 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:04:22s. Time for last 1,000,000: 3s. Last read position: chr6:32,126,191
INFO 2026-05-28 00:05:10 MarkDuplicates Tracking 192617 as yet unmatched pairs. 9354 records in RAM.
INFO 2026-05-28 00:05:13 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:04:25s. Time for last 1,000,000: 3s. Last read position: chr6:34,240,853
INFO 2026-05-28 00:05:13 MarkDuplicates Tracking 191020 as yet unmatched pairs. 7756 records in RAM.
INFO 2026-05-28 00:05:17 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:04:29s. Time for last 1,000,000: 3s. Last read position: chr6:43,516,078
INFO 2026-05-28 00:05:17 MarkDuplicates Tracking 189587 as yet unmatched pairs. 6322 records in RAM.
INFO 2026-05-28 00:05:21 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:04:33s. Time for last 1,000,000: 4s. Last read position: chr6:70,528,355
INFO 2026-05-28 00:05:21 MarkDuplicates Tracking 188328 as yet unmatched pairs. 5063 records in RAM.
INFO 2026-05-28 00:05:25 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:04:37s. Time for last 1,000,000: 3s. Last read position: chr6:106,971,379
INFO 2026-05-28 00:05:25 MarkDuplicates Tracking 187849 as yet unmatched pairs. 4581 records in RAM.
INFO 2026-05-28 00:05:29 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:04:41s. Time for last 1,000,000: 3s. Last read position: chr6:136,388,417
INFO 2026-05-28 00:05:29 MarkDuplicates Tracking 185776 as yet unmatched pairs. 2507 records in RAM.
INFO 2026-05-28 00:05:33 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:04:45s. Time for last 1,000,000: 3s. Last read position: chr6:158,573,420
INFO 2026-05-28 00:05:33 MarkDuplicates Tracking 184594 as yet unmatched pairs. 1325 records in RAM.
INFO 2026-05-28 00:05:37 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:04:49s. Time for last 1,000,000: 3s. Last read position: chr7:1,057,688
INFO 2026-05-28 00:05:37 MarkDuplicates Tracking 183044 as yet unmatched pairs. 13363 records in RAM.
INFO 2026-05-28 00:05:40 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:04:52s. Time for last 1,000,000: 3s. Last read position: chr7:5,528,510
INFO 2026-05-28 00:05:40 MarkDuplicates Tracking 183115 as yet unmatched pairs. 13434 records in RAM.
INFO 2026-05-28 00:05:43 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:04:55s. Time for last 1,000,000: 3s. Last read position: chr7:26,152,738
INFO 2026-05-28 00:05:43 MarkDuplicates Tracking 180324 as yet unmatched pairs. 10643 records in RAM.
INFO 2026-05-28 00:05:47 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:04:59s. Time for last 1,000,000: 3s. Last read position: chr7:47,293,795
INFO 2026-05-28 00:05:47 MarkDuplicates Tracking 178926 as yet unmatched pairs. 9245 records in RAM.
INFO 2026-05-28 00:05:51 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:05:03s. Time for last 1,000,000: 4s. Last read position: chr7:74,746,366
INFO 2026-05-28 00:05:51 MarkDuplicates Tracking 177648 as yet unmatched pairs. 7967 records in RAM.
INFO 2026-05-28 00:05:55 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:05:07s. Time for last 1,000,000: 3s. Last read position: chr7:94,400,201
INFO 2026-05-28 00:05:55 MarkDuplicates Tracking 176629 as yet unmatched pairs. 6948 records in RAM.
INFO 2026-05-28 00:05:58 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:05:10s. Time for last 1,000,000: 3s. Last read position: chr7:100,607,958
INFO 2026-05-28 00:05:58 MarkDuplicates Tracking 175116 as yet unmatched pairs. 5435 records in RAM.
INFO 2026-05-28 00:06:01 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:05:13s. Time for last 1,000,000: 3s. Last read position: chr7:101,000,129
INFO 2026-05-28 00:06:01 MarkDuplicates Tracking 174431 as yet unmatched pairs. 4749 records in RAM.
INFO 2026-05-28 00:06:05 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:05:17s. Time for last 1,000,000: 3s. Last read position: chr7:107,210,555
INFO 2026-05-28 00:06:05 MarkDuplicates Tracking 173436 as yet unmatched pairs. 3754 records in RAM.
INFO 2026-05-28 00:06:08 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:05:20s. Time for last 1,000,000: 3s. Last read position: chr7:129,832,139
INFO 2026-05-28 00:06:08 MarkDuplicates Tracking 172163 as yet unmatched pairs. 2481 records in RAM.
INFO 2026-05-28 00:06:11 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:05:23s. Time for last 1,000,000: 3s. Last read position: chr7:144,267,706
INFO 2026-05-28 00:06:11 MarkDuplicates Tracking 171145 as yet unmatched pairs. 1460 records in RAM.
INFO 2026-05-28 00:06:15 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:05:27s. Time for last 1,000,000: 3s. Last read position: chr7:158,138,326
INFO 2026-05-28 00:06:15 MarkDuplicates Tracking 169866 as yet unmatched pairs. 181 records in RAM.
INFO 2026-05-28 00:06:19 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:05:31s. Time for last 1,000,000: 3s. Last read position: chr8:22,617,490
INFO 2026-05-28 00:06:19 MarkDuplicates Tracking 168518 as yet unmatched pairs. 10953 records in RAM.
INFO 2026-05-28 00:06:23 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:05:35s. Time for last 1,000,000: 3s. Last read position: chr8:38,210,049
INFO 2026-05-28 00:06:23 MarkDuplicates Tracking 166985 as yet unmatched pairs. 9419 records in RAM.
INFO 2026-05-28 00:06:27 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:05:39s. Time for last 1,000,000: 4s. Last read position: chr8:54,135,271
INFO 2026-05-28 00:06:27 MarkDuplicates Tracking 165598 as yet unmatched pairs. 8031 records in RAM.
INFO 2026-05-28 00:06:31 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:05:43s. Time for last 1,000,000: 3s. Last read position: chr8:81,732,770
INFO 2026-05-28 00:06:31 MarkDuplicates Tracking 164440 as yet unmatched pairs. 6873 records in RAM.
INFO 2026-05-28 00:06:34 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:05:47s. Time for last 1,000,000: 3s. Last read position: chr8:100,718,206
INFO 2026-05-28 00:06:34 MarkDuplicates Tracking 164455 as yet unmatched pairs. 6887 records in RAM.
INFO 2026-05-28 00:06:38 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:05:50s. Time for last 1,000,000: 3s. Last read position: chr8:126,556,528
INFO 2026-05-28 00:06:38 MarkDuplicates Tracking 161759 as yet unmatched pairs. 4190 records in RAM.
INFO 2026-05-28 00:06:41 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:05:53s. Time for last 1,000,000: 3s. Last read position: chr8:143,860,441
INFO 2026-05-28 00:06:41 MarkDuplicates Tracking 160433 as yet unmatched pairs. 2864 records in RAM.
INFO 2026-05-28 00:06:45 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:05:57s. Time for last 1,000,000: 3s. Last read position: chr8:143,934,360
INFO 2026-05-28 00:06:45 MarkDuplicates Tracking 159007 as yet unmatched pairs. 1437 records in RAM.
INFO 2026-05-28 00:06:48 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:06:00s. Time for last 1,000,000: 3s. Last read position: chr9:5,921,091
INFO 2026-05-28 00:06:48 MarkDuplicates Tracking 157383 as yet unmatched pairs. 9785 records in RAM.
INFO 2026-05-28 00:06:52 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:06:04s. Time for last 1,000,000: 3s. Last read position: chr9:35,752,699
INFO 2026-05-28 00:06:52 MarkDuplicates Tracking 155977 as yet unmatched pairs. 8377 records in RAM.
INFO 2026-05-28 00:06:56 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:06:08s. Time for last 1,000,000: 3s. Last read position: chr9:89,001,977
INFO 2026-05-28 00:06:56 MarkDuplicates Tracking 154736 as yet unmatched pairs. 7130 records in RAM.
INFO 2026-05-28 00:06:59 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:06:11s. Time for last 1,000,000: 3s. Last read position: chr9:107,487,309
INFO 2026-05-28 00:06:59 MarkDuplicates Tracking 153585 as yet unmatched pairs. 5978 records in RAM.
INFO 2026-05-28 00:07:02 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:06:14s. Time for last 1,000,000: 2s. Last read position: chr9:122,998,632
INFO 2026-05-28 00:07:02 MarkDuplicates Tracking 152067 as yet unmatched pairs. 4459 records in RAM.
INFO 2026-05-28 00:07:06 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:06:18s. Time for last 1,000,000: 3s. Last read position: chr9:128,691,872
INFO 2026-05-28 00:07:06 MarkDuplicates Tracking 151226 as yet unmatched pairs. 3617 records in RAM.
INFO 2026-05-28 00:07:10 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:06:22s. Time for last 1,000,000: 3s. Last read position: chr9:134,045,337
INFO 2026-05-28 00:07:10 MarkDuplicates Tracking 149366 as yet unmatched pairs. 1757 records in RAM.
INFO 2026-05-28 00:07:13 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:06:25s. Time for last 1,000,000: 3s. Last read position: chr9:137,605,720
INFO 2026-05-28 00:07:13 MarkDuplicates Tracking 147810 as yet unmatched pairs. 200 records in RAM.
INFO 2026-05-28 00:07:17 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:06:29s. Time for last 1,000,000: 4s. Last read position: chr10:22,318,957
INFO 2026-05-28 00:07:17 MarkDuplicates Tracking 146588 as yet unmatched pairs. 9940 records in RAM.
INFO 2026-05-28 00:07:21 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:06:33s. Time for last 1,000,000: 3s. Last read position: chr10:32,039,404
INFO 2026-05-28 00:07:21 MarkDuplicates Tracking 146356 as yet unmatched pairs. 9708 records in RAM.
INFO 2026-05-28 00:07:25 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:06:37s. Time for last 1,000,000: 4s. Last read position: chr10:56,358,823
INFO 2026-05-28 00:07:25 MarkDuplicates Tracking 144268 as yet unmatched pairs. 7620 records in RAM.
INFO 2026-05-28 00:07:29 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:06:41s. Time for last 1,000,000: 4s. Last read position: chr10:73,792,247
INFO 2026-05-28 00:07:29 MarkDuplicates Tracking 143055 as yet unmatched pairs. 6405 records in RAM.
INFO 2026-05-28 00:07:33 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:06:45s. Time for last 1,000,000: 3s. Last read position: chr10:87,933,082
INFO 2026-05-28 00:07:33 MarkDuplicates Tracking 141877 as yet unmatched pairs. 5227 records in RAM.
INFO 2026-05-28 00:07:36 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:06:48s. Time for last 1,000,000: 3s. Last read position: chr10:98,435,351
INFO 2026-05-28 00:07:36 MarkDuplicates Tracking 140550 as yet unmatched pairs. 3899 records in RAM.
INFO 2026-05-28 00:07:40 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:06:52s. Time for last 1,000,000: 3s. Last read position: chr10:104,055,884
INFO 2026-05-28 00:07:40 MarkDuplicates Tracking 139038 as yet unmatched pairs. 2386 records in RAM.
INFO 2026-05-28 00:07:43 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:06:55s. Time for last 1,000,000: 3s. Last read position: chr10:120,860,248
INFO 2026-05-28 00:07:43 MarkDuplicates Tracking 137673 as yet unmatched pairs. 1020 records in RAM.
INFO 2026-05-28 00:07:47 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:06:59s. Time for last 1,000,000: 3s. Last read position: chr11:396,645
INFO 2026-05-28 00:07:47 MarkDuplicates Tracking 136450 as yet unmatched pairs. 20426 records in RAM.
INFO 2026-05-28 00:07:51 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:07:03s. Time for last 1,000,000: 4s. Last read position: chr11:1,090,823
INFO 2026-05-28 00:07:51 MarkDuplicates Tracking 135157 as yet unmatched pairs. 19133 records in RAM.
INFO 2026-05-28 00:07:54 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:07:06s. Time for last 1,000,000: 3s. Last read position: chr11:1,191,760
INFO 2026-05-28 00:07:54 MarkDuplicates Tracking 134177 as yet unmatched pairs. 18150 records in RAM.
INFO 2026-05-28 00:07:57 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:07:09s. Time for last 1,000,000: 3s. Last read position: chr11:1,753,630
INFO 2026-05-28 00:07:57 MarkDuplicates Tracking 133289 as yet unmatched pairs. 17261 records in RAM.
INFO 2026-05-28 00:08:01 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:07:13s. Time for last 1,000,000: 3s. Last read position: chr11:9,585,273
INFO 2026-05-28 00:08:01 MarkDuplicates Tracking 131385 as yet unmatched pairs. 15357 records in RAM.
INFO 2026-05-28 00:08:03 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:07:15s. Time for last 1,000,000: 2s. Last read position: chr11:32,593,879
INFO 2026-05-28 00:08:03 MarkDuplicates Tracking 130360 as yet unmatched pairs. 14332 records in RAM.
INFO 2026-05-28 00:08:05 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:07:17s. Time for last 1,000,000: 2s. Last read position: chr11:47,324,298
INFO 2026-05-28 00:08:05 MarkDuplicates Tracking 128893 as yet unmatched pairs. 12865 records in RAM.
INFO 2026-05-28 00:08:08 MarkDuplicates Read 117,000,000 records. Elapsed time: 00:07:20s. Time for last 1,000,000: 2s. Last read position: chr11:61,965,398
INFO 2026-05-28 00:08:08 MarkDuplicates Tracking 128818 as yet unmatched pairs. 12789 records in RAM.
INFO 2026-05-28 00:08:11 MarkDuplicates Read 118,000,000 records. Elapsed time: 00:07:23s. Time for last 1,000,000: 2s. Last read position: chr11:62,571,080
INFO 2026-05-28 00:08:11 MarkDuplicates Tracking 126470 as yet unmatched pairs. 10441 records in RAM.
INFO 2026-05-28 00:08:13 MarkDuplicates Read 119,000,000 records. Elapsed time: 00:07:25s. Time for last 1,000,000: 2s. Last read position: chr11:64,906,445
INFO 2026-05-28 00:08:13 MarkDuplicates Tracking 124716 as yet unmatched pairs. 8686 records in RAM.
INFO 2026-05-28 00:08:15 MarkDuplicates Read 120,000,000 records. Elapsed time: 00:07:27s. Time for last 1,000,000: 2s. Last read position: chr11:66,271,847
INFO 2026-05-28 00:08:15 MarkDuplicates Tracking 123334 as yet unmatched pairs. 7303 records in RAM.
INFO 2026-05-28 00:08:18 MarkDuplicates Read 121,000,000 records. Elapsed time: 00:07:30s. Time for last 1,000,000: 2s. Last read position: chr11:68,043,571
INFO 2026-05-28 00:08:18 MarkDuplicates Tracking 121714 as yet unmatched pairs. 5682 records in RAM.
INFO 2026-05-28 00:08:21 MarkDuplicates Read 122,000,000 records. Elapsed time: 00:07:33s. Time for last 1,000,000: 3s. Last read position: chr11:72,013,039
INFO 2026-05-28 00:08:21 MarkDuplicates Tracking 120311 as yet unmatched pairs. 4279 records in RAM.
INFO 2026-05-28 00:08:23 MarkDuplicates Read 123,000,000 records. Elapsed time: 00:07:36s. Time for last 1,000,000: 2s. Last read position: chr11:78,101,181
INFO 2026-05-28 00:08:23 MarkDuplicates Tracking 118798 as yet unmatched pairs. 2765 records in RAM.
INFO 2026-05-28 00:08:26 MarkDuplicates Read 124,000,000 records. Elapsed time: 00:07:38s. Time for last 1,000,000: 2s. Last read position: chr11:117,098,211
INFO 2026-05-28 00:08:26 MarkDuplicates Tracking 117615 as yet unmatched pairs. 1581 records in RAM.
INFO 2026-05-28 00:08:29 MarkDuplicates Read 125,000,000 records. Elapsed time: 00:07:41s. Time for last 1,000,000: 2s. Last read position: chr11:129,855,703
INFO 2026-05-28 00:08:29 MarkDuplicates Tracking 116323 as yet unmatched pairs. 289 records in RAM.
INFO 2026-05-28 00:08:31 MarkDuplicates Read 126,000,000 records. Elapsed time: 00:07:43s. Time for last 1,000,000: 2s. Last read position: chr12:6,752,284
INFO 2026-05-28 00:08:31 MarkDuplicates Tracking 115029 as yet unmatched pairs. 13372 records in RAM.
INFO 2026-05-28 00:08:34 MarkDuplicates Read 127,000,000 records. Elapsed time: 00:07:46s. Time for last 1,000,000: 2s. Last read position: chr12:14,795,009
INFO 2026-05-28 00:08:34 MarkDuplicates Tracking 113764 as yet unmatched pairs. 12106 records in RAM.
INFO 2026-05-28 00:08:36 MarkDuplicates Read 128,000,000 records. Elapsed time: 00:07:48s. Time for last 1,000,000: 2s. Last read position: chr12:48,343,083
INFO 2026-05-28 00:08:36 MarkDuplicates Tracking 112435 as yet unmatched pairs. 10777 records in RAM.
INFO 2026-05-28 00:08:39 MarkDuplicates Read 129,000,000 records. Elapsed time: 00:07:51s. Time for last 1,000,000: 3s. Last read position: chr12:52,011,042
INFO 2026-05-28 00:08:39 MarkDuplicates Tracking 111310 as yet unmatched pairs. 9645 records in RAM.
INFO 2026-05-28 00:08:41 MarkDuplicates Read 130,000,000 records. Elapsed time: 00:07:53s. Time for last 1,000,000: 2s. Last read position: chr12:54,281,465
INFO 2026-05-28 00:08:41 MarkDuplicates Tracking 110752 as yet unmatched pairs. 9087 records in RAM.
INFO 2026-05-28 00:08:45 MarkDuplicates Read 131,000,000 records. Elapsed time: 00:07:57s. Time for last 1,000,000: 3s. Last read position: chr12:56,643,486
INFO 2026-05-28 00:08:45 MarkDuplicates Tracking 109261 as yet unmatched pairs. 7596 records in RAM.
INFO 2026-05-28 00:08:48 MarkDuplicates Read 132,000,000 records. Elapsed time: 00:08:00s. Time for last 1,000,000: 3s. Last read position: chr12:57,716,483
INFO 2026-05-28 00:08:48 MarkDuplicates Tracking 107898 as yet unmatched pairs. 6233 records in RAM.
INFO 2026-05-28 00:08:52 MarkDuplicates Read 133,000,000 records. Elapsed time: 00:08:04s. Time for last 1,000,000: 3s. Last read position: chr12:82,357,099
INFO 2026-05-28 00:08:52 MarkDuplicates Tracking 106581 as yet unmatched pairs. 4916 records in RAM.
INFO 2026-05-28 00:08:54 MarkDuplicates Read 134,000,000 records. Elapsed time: 00:08:06s. Time for last 1,000,000: 2s. Last read position: chr12:108,567,189
INFO 2026-05-28 00:08:54 MarkDuplicates Tracking 105477 as yet unmatched pairs. 3811 records in RAM.
INFO 2026-05-28 00:08:57 MarkDuplicates Read 135,000,000 records. Elapsed time: 00:08:09s. Time for last 1,000,000: 2s. Last read position: chr12:118,036,357
INFO 2026-05-28 00:08:57 MarkDuplicates Tracking 104210 as yet unmatched pairs. 2544 records in RAM.
INFO 2026-05-28 00:08:59 MarkDuplicates Read 136,000,000 records. Elapsed time: 00:08:11s. Time for last 1,000,000: 2s. Last read position: chr12:124,012,865
INFO 2026-05-28 00:08:59 MarkDuplicates Tracking 102726 as yet unmatched pairs. 1059 records in RAM.
INFO 2026-05-28 00:09:02 MarkDuplicates Read 137,000,000 records. Elapsed time: 00:08:14s. Time for last 1,000,000: 2s. Last read position: chr13:24,434,905
INFO 2026-05-28 00:09:02 MarkDuplicates Tracking 101672 as yet unmatched pairs. 3209 records in RAM.
INFO 2026-05-28 00:09:06 MarkDuplicates Read 138,000,000 records. Elapsed time: 00:08:18s. Time for last 1,000,000: 3s. Last read position: chr13:49,701,890
INFO 2026-05-28 00:09:06 MarkDuplicates Tracking 100281 as yet unmatched pairs. 1818 records in RAM.
INFO 2026-05-28 00:09:08 MarkDuplicates Read 139,000,000 records. Elapsed time: 00:08:20s. Time for last 1,000,000: 2s. Last read position: chr13:110,506,565
INFO 2026-05-28 00:09:08 MarkDuplicates Tracking 99020 as yet unmatched pairs. 556 records in RAM.
INFO 2026-05-28 00:09:10 MarkDuplicates Read 140,000,000 records. Elapsed time: 00:08:22s. Time for last 1,000,000: 2s. Last read position: chr14:24,182,376
INFO 2026-05-28 00:09:10 MarkDuplicates Tracking 97538 as yet unmatched pairs. 6467 records in RAM.
INFO 2026-05-28 00:09:12 MarkDuplicates Read 141,000,000 records. Elapsed time: 00:08:24s. Time for last 1,000,000: 2s. Last read position: chr14:58,215,263
INFO 2026-05-28 00:09:12 MarkDuplicates Tracking 96331 as yet unmatched pairs. 5260 records in RAM.
INFO 2026-05-28 00:09:15 MarkDuplicates Read 142,000,000 records. Elapsed time: 00:08:27s. Time for last 1,000,000: 2s. Last read position: chr14:74,911,288
INFO 2026-05-28 00:09:15 MarkDuplicates Tracking 95056 as yet unmatched pairs. 3982 records in RAM.
INFO 2026-05-28 00:09:17 MarkDuplicates Read 143,000,000 records. Elapsed time: 00:08:29s. Time for last 1,000,000: 2s. Last read position: chr14:102,043,921
INFO 2026-05-28 00:09:17 MarkDuplicates Tracking 93747 as yet unmatched pairs. 2667 records in RAM.
INFO 2026-05-28 00:09:19 MarkDuplicates Read 144,000,000 records. Elapsed time: 00:08:31s. Time for last 1,000,000: 2s. Last read position: chr14:105,587,638
INFO 2026-05-28 00:09:19 MarkDuplicates Tracking 94416 as yet unmatched pairs. 3330 records in RAM.
INFO 2026-05-28 00:09:22 MarkDuplicates Read 145,000,000 records. Elapsed time: 00:08:34s. Time for last 1,000,000: 2s. Last read position: chr14:105,855,915
INFO 2026-05-28 00:09:22 MarkDuplicates Tracking 91567 as yet unmatched pairs. 481 records in RAM.
INFO 2026-05-28 00:09:24 MarkDuplicates Read 146,000,000 records. Elapsed time: 00:08:36s. Time for last 1,000,000: 2s. Last read position: chr15:40,354,352
INFO 2026-05-28 00:09:24 MarkDuplicates Tracking 90434 as yet unmatched pairs. 7483 records in RAM.
INFO 2026-05-28 00:09:26 MarkDuplicates Read 147,000,000 records. Elapsed time: 00:08:38s. Time for last 1,000,000: 2s. Last read position: chr15:44,663,543
INFO 2026-05-28 00:09:26 MarkDuplicates Tracking 88820 as yet unmatched pairs. 5869 records in RAM.
INFO 2026-05-28 00:09:28 MarkDuplicates Read 148,000,000 records. Elapsed time: 00:08:40s. Time for last 1,000,000: 2s. Last read position: chr15:60,448,040
INFO 2026-05-28 00:09:28 MarkDuplicates Tracking 87633 as yet unmatched pairs. 4682 records in RAM.
INFO 2026-05-28 00:09:30 MarkDuplicates Read 149,000,000 records. Elapsed time: 00:08:43s. Time for last 1,000,000: 2s. Last read position: chr15:70,668,741
INFO 2026-05-28 00:09:30 MarkDuplicates Tracking 86206 as yet unmatched pairs. 3255 records in RAM.
INFO 2026-05-28 00:09:33 MarkDuplicates Read 150,000,000 records. Elapsed time: 00:08:45s. Time for last 1,000,000: 2s. Last read position: chr15:78,922,083
INFO 2026-05-28 00:09:33 MarkDuplicates Tracking 84852 as yet unmatched pairs. 1900 records in RAM.
INFO 2026-05-28 00:09:35 MarkDuplicates Read 151,000,000 records. Elapsed time: 00:08:47s. Time for last 1,000,000: 2s. Last read position: chr15:90,906,775
INFO 2026-05-28 00:09:35 MarkDuplicates Tracking 83554 as yet unmatched pairs. 602 records in RAM.
INFO 2026-05-28 00:09:37 MarkDuplicates Read 152,000,000 records. Elapsed time: 00:08:49s. Time for last 1,000,000: 2s. Last read position: chr16:1,961,797
INFO 2026-05-28 00:09:37 MarkDuplicates Tracking 81986 as yet unmatched pairs. 14168 records in RAM.
INFO 2026-05-28 00:09:39 MarkDuplicates Read 153,000,000 records. Elapsed time: 00:08:51s. Time for last 1,000,000: 2s. Last read position: chr16:8,899,131
INFO 2026-05-28 00:09:39 MarkDuplicates Tracking 80570 as yet unmatched pairs. 12752 records in RAM.
INFO 2026-05-28 00:09:41 MarkDuplicates Read 154,000,000 records. Elapsed time: 00:08:53s. Time for last 1,000,000: 1s. Last read position: chr16:15,724,166
INFO 2026-05-28 00:09:41 MarkDuplicates Tracking 79795 as yet unmatched pairs. 11977 records in RAM.
INFO 2026-05-28 00:09:43 MarkDuplicates Read 155,000,000 records. Elapsed time: 00:08:55s. Time for last 1,000,000: 1s. Last read position: chr16:18,351,301
INFO 2026-05-28 00:09:43 MarkDuplicates Tracking 78945 as yet unmatched pairs. 11127 records in RAM.
INFO 2026-05-28 00:09:45 MarkDuplicates Read 156,000,000 records. Elapsed time: 00:08:57s. Time for last 1,000,000: 2s. Last read position: chr16:21,405,342
INFO 2026-05-28 00:09:45 MarkDuplicates Tracking 77975 as yet unmatched pairs. 10156 records in RAM.
INFO 2026-05-28 00:09:47 MarkDuplicates Read 157,000,000 records. Elapsed time: 00:08:59s. Time for last 1,000,000: 2s. Last read position: chr16:23,587,212
INFO 2026-05-28 00:09:47 MarkDuplicates Tracking 77394 as yet unmatched pairs. 9575 records in RAM.
INFO 2026-05-28 00:09:49 MarkDuplicates Read 158,000,000 records. Elapsed time: 00:09:01s. Time for last 1,000,000: 2s. Last read position: chr16:28,835,735
INFO 2026-05-28 00:09:49 MarkDuplicates Tracking 76338 as yet unmatched pairs. 8519 records in RAM.
INFO 2026-05-28 00:09:51 MarkDuplicates Read 159,000,000 records. Elapsed time: 00:09:03s. Time for last 1,000,000: 2s. Last read position: chr16:29,896,987
INFO 2026-05-28 00:09:51 MarkDuplicates Tracking 75235 as yet unmatched pairs. 7414 records in RAM.
INFO 2026-05-28 00:09:53 MarkDuplicates Read 160,000,000 records. Elapsed time: 00:09:05s. Time for last 1,000,000: 1s. Last read position: chr16:30,724,436
INFO 2026-05-28 00:09:53 MarkDuplicates Tracking 74033 as yet unmatched pairs. 6212 records in RAM.
INFO 2026-05-28 00:09:56 MarkDuplicates Read 161,000,000 records. Elapsed time: 00:09:08s. Time for last 1,000,000: 2s. Last read position: chr16:56,683,212
INFO 2026-05-28 00:09:56 MarkDuplicates Tracking 73058 as yet unmatched pairs. 5237 records in RAM.
INFO 2026-05-28 00:09:58 MarkDuplicates Read 162,000,000 records. Elapsed time: 00:09:10s. Time for last 1,000,000: 1s. Last read position: chr16:68,235,949
INFO 2026-05-28 00:09:58 MarkDuplicates Tracking 71144 as yet unmatched pairs. 3323 records in RAM.
INFO 2026-05-28 00:10:00 MarkDuplicates Read 163,000,000 records. Elapsed time: 00:09:12s. Time for last 1,000,000: 2s. Last read position: chr16:75,242,800
INFO 2026-05-28 00:10:00 MarkDuplicates Tracking 70090 as yet unmatched pairs. 2269 records in RAM.
INFO 2026-05-28 00:10:02 MarkDuplicates Read 164,000,000 records. Elapsed time: 00:09:14s. Time for last 1,000,000: 2s. Last read position: chr16:89,561,224
INFO 2026-05-28 00:10:02 MarkDuplicates Tracking 68814 as yet unmatched pairs. 988 records in RAM.
INFO 2026-05-28 00:10:04 MarkDuplicates Read 165,000,000 records. Elapsed time: 00:09:16s. Time for last 1,000,000: 2s. Last read position: chr17:4,554,220
INFO 2026-05-28 00:10:04 MarkDuplicates Tracking 66818 as yet unmatched pairs. 18768 records in RAM.
INFO 2026-05-28 00:10:06 MarkDuplicates Read 166,000,000 records. Elapsed time: 00:09:19s. Time for last 1,000,000: 2s. Last read position: chr17:7,856,708
INFO 2026-05-28 00:10:06 MarkDuplicates Tracking 65510 as yet unmatched pairs. 17460 records in RAM.
INFO 2026-05-28 00:10:09 MarkDuplicates Read 167,000,000 records. Elapsed time: 00:09:21s. Time for last 1,000,000: 2s. Last read position: chr17:27,647,099
INFO 2026-05-28 00:10:09 MarkDuplicates Tracking 64362 as yet unmatched pairs. 16312 records in RAM.
INFO 2026-05-28 00:10:11 MarkDuplicates Read 168,000,000 records. Elapsed time: 00:09:23s. Time for last 1,000,000: 2s. Last read position: chr17:35,363,468
INFO 2026-05-28 00:10:11 MarkDuplicates Tracking 62830 as yet unmatched pairs. 14780 records in RAM.
INFO 2026-05-28 00:10:13 MarkDuplicates Read 169,000,000 records. Elapsed time: 00:09:25s. Time for last 1,000,000: 2s. Last read position: chr17:39,700,300
INFO 2026-05-28 00:10:13 MarkDuplicates Tracking 62098 as yet unmatched pairs. 14048 records in RAM.
INFO 2026-05-28 00:10:15 MarkDuplicates Read 170,000,000 records. Elapsed time: 00:09:27s. Time for last 1,000,000: 1s. Last read position: chr17:41,763,216
INFO 2026-05-28 00:10:15 MarkDuplicates Tracking 60377 as yet unmatched pairs. 12327 records in RAM.
INFO 2026-05-28 00:10:17 MarkDuplicates Read 171,000,000 records. Elapsed time: 00:09:29s. Time for last 1,000,000: 2s. Last read position: chr17:44,784,338
INFO 2026-05-28 00:10:17 MarkDuplicates Tracking 58632 as yet unmatched pairs. 10582 records in RAM.
INFO 2026-05-28 00:10:20 MarkDuplicates Read 172,000,000 records. Elapsed time: 00:09:32s. Time for last 1,000,000: 2s. Last read position: chr17:50,186,878
INFO 2026-05-28 00:10:20 MarkDuplicates Tracking 58184 as yet unmatched pairs. 10134 records in RAM.
INFO 2026-05-28 00:10:22 MarkDuplicates Read 173,000,000 records. Elapsed time: 00:09:34s. Time for last 1,000,000: 2s. Last read position: chr17:50,196,493
INFO 2026-05-28 00:10:22 MarkDuplicates Tracking 56970 as yet unmatched pairs. 8920 records in RAM.
INFO 2026-05-28 00:10:24 MarkDuplicates Read 174,000,000 records. Elapsed time: 00:09:36s. Time for last 1,000,000: 2s. Last read position: chr17:59,570,537
INFO 2026-05-28 00:10:24 MarkDuplicates Tracking 54564 as yet unmatched pairs. 6514 records in RAM.
INFO 2026-05-28 00:10:26 MarkDuplicates Read 175,000,000 records. Elapsed time: 00:09:38s. Time for last 1,000,000: 2s. Last read position: chr17:66,732,741
INFO 2026-05-28 00:10:26 MarkDuplicates Tracking 53340 as yet unmatched pairs. 5289 records in RAM.
INFO 2026-05-28 00:10:29 MarkDuplicates Read 176,000,000 records. Elapsed time: 00:09:41s. Time for last 1,000,000: 2s. Last read position: chr17:75,730,298
INFO 2026-05-28 00:10:29 MarkDuplicates Tracking 52206 as yet unmatched pairs. 4154 records in RAM.
INFO 2026-05-28 00:10:31 MarkDuplicates Read 177,000,000 records. Elapsed time: 00:09:43s. Time for last 1,000,000: 2s. Last read position: chr17:78,803,595
INFO 2026-05-28 00:10:31 MarkDuplicates Tracking 50467 as yet unmatched pairs. 2413 records in RAM.
INFO 2026-05-28 00:10:33 MarkDuplicates Read 178,000,000 records. Elapsed time: 00:09:45s. Time for last 1,000,000: 1s. Last read position: chr17:81,868,296
INFO 2026-05-28 00:10:33 MarkDuplicates Tracking 49253 as yet unmatched pairs. 1199 records in RAM.
INFO 2026-05-28 00:10:35 MarkDuplicates Read 179,000,000 records. Elapsed time: 00:09:47s. Time for last 1,000,000: 2s. Last read position: chr18:13,742,568
INFO 2026-05-28 00:10:35 MarkDuplicates Tracking 47523 as yet unmatched pairs. 1870 records in RAM.
INFO 2026-05-28 00:10:37 MarkDuplicates Read 180,000,000 records. Elapsed time: 00:09:49s. Time for last 1,000,000: 2s. Last read position: chr18:58,948,156
INFO 2026-05-28 00:10:37 MarkDuplicates Tracking 46193 as yet unmatched pairs. 540 records in RAM.
INFO 2026-05-28 00:10:40 MarkDuplicates Read 181,000,000 records. Elapsed time: 00:09:52s. Time for last 1,000,000: 2s. Last read position: chr19:1,438,866
INFO 2026-05-28 00:10:40 MarkDuplicates Tracking 45604 as yet unmatched pairs. 20322 records in RAM.
INFO 2026-05-28 00:10:42 MarkDuplicates Read 182,000,000 records. Elapsed time: 00:09:54s. Time for last 1,000,000: 2s. Last read position: chr19:5,690,442
INFO 2026-05-28 00:10:42 MarkDuplicates Tracking 43068 as yet unmatched pairs. 17786 records in RAM.
INFO 2026-05-28 00:10:44 MarkDuplicates Read 183,000,000 records. Elapsed time: 00:09:56s. Time for last 1,000,000: 2s. Last read position: chr19:10,546,862
INFO 2026-05-28 00:10:44 MarkDuplicates Tracking 41526 as yet unmatched pairs. 16244 records in RAM.
INFO 2026-05-28 00:10:46 MarkDuplicates Read 184,000,000 records. Elapsed time: 00:09:59s. Time for last 1,000,000: 2s. Last read position: chr19:14,464,131
INFO 2026-05-28 00:10:46 MarkDuplicates Tracking 40136 as yet unmatched pairs. 14854 records in RAM.
INFO 2026-05-28 00:10:48 MarkDuplicates Read 185,000,000 records. Elapsed time: 00:10:00s. Time for last 1,000,000: 1s. Last read position: chr19:18,465,421
INFO 2026-05-28 00:10:48 MarkDuplicates Tracking 38487 as yet unmatched pairs. 13205 records in RAM.
INFO 2026-05-28 00:10:51 MarkDuplicates Read 186,000,000 records. Elapsed time: 00:10:03s. Time for last 1,000,000: 2s. Last read position: chr19:35,651,247
INFO 2026-05-28 00:10:51 MarkDuplicates Tracking 37302 as yet unmatched pairs. 12020 records in RAM.
INFO 2026-05-28 00:10:53 MarkDuplicates Read 187,000,000 records. Elapsed time: 00:10:05s. Time for last 1,000,000: 2s. Last read position: chr19:38,845,659
INFO 2026-05-28 00:10:53 MarkDuplicates Tracking 35845 as yet unmatched pairs. 10563 records in RAM.
INFO 2026-05-28 00:10:55 MarkDuplicates Read 188,000,000 records. Elapsed time: 00:10:07s. Time for last 1,000,000: 2s. Last read position: chr19:39,889,612
INFO 2026-05-28 00:10:55 MarkDuplicates Tracking 34875 as yet unmatched pairs. 9593 records in RAM.
INFO 2026-05-28 00:10:57 MarkDuplicates Read 189,000,000 records. Elapsed time: 00:10:09s. Time for last 1,000,000: 2s. Last read position: chr19:40,465,621
INFO 2026-05-28 00:10:57 MarkDuplicates Tracking 33133 as yet unmatched pairs. 7851 records in RAM.
INFO 2026-05-28 00:10:59 MarkDuplicates Read 190,000,000 records. Elapsed time: 00:10:11s. Time for last 1,000,000: 1s. Last read position: chr19:42,274,434
INFO 2026-05-28 00:10:59 MarkDuplicates Tracking 31920 as yet unmatched pairs. 6638 records in RAM.
INFO 2026-05-28 00:11:01 MarkDuplicates Read 191,000,000 records. Elapsed time: 00:10:13s. Time for last 1,000,000: 2s. Last read position: chr19:46,756,706
INFO 2026-05-28 00:11:01 MarkDuplicates Tracking 30201 as yet unmatched pairs. 4914 records in RAM.
INFO 2026-05-28 00:11:03 MarkDuplicates Read 192,000,000 records. Elapsed time: 00:10:15s. Time for last 1,000,000: 2s. Last read position: chr19:49,497,264
INFO 2026-05-28 00:11:03 MarkDuplicates Tracking 29453 as yet unmatched pairs. 4166 records in RAM.
INFO 2026-05-28 00:11:06 MarkDuplicates Read 193,000,000 records. Elapsed time: 00:10:18s. Time for last 1,000,000: 2s. Last read position: chr19:53,068,655
INFO 2026-05-28 00:11:06 MarkDuplicates Tracking 27112 as yet unmatched pairs. 1825 records in RAM.
INFO 2026-05-28 00:11:08 MarkDuplicates Read 194,000,000 records. Elapsed time: 00:10:20s. Time for last 1,000,000: 2s. Last read position: chr19:58,090,124
INFO 2026-05-28 00:11:08 MarkDuplicates Tracking 25692 as yet unmatched pairs. 405 records in RAM.
INFO 2026-05-28 00:11:10 MarkDuplicates Read 195,000,000 records. Elapsed time: 00:10:22s. Time for last 1,000,000: 2s. Last read position: chr20:17,600,813
INFO 2026-05-28 00:11:10 MarkDuplicates Tracking 24556 as yet unmatched pairs. 6005 records in RAM.
INFO 2026-05-28 00:11:12 MarkDuplicates Read 196,000,000 records. Elapsed time: 00:10:24s. Time for last 1,000,000: 2s. Last read position: chr20:33,811,597
INFO 2026-05-28 00:11:12 MarkDuplicates Tracking 22912 as yet unmatched pairs. 4361 records in RAM.
INFO 2026-05-28 00:11:14 MarkDuplicates Read 197,000,000 records. Elapsed time: 00:10:26s. Time for last 1,000,000: 2s. Last read position: chr20:44,424,237
INFO 2026-05-28 00:11:14 MarkDuplicates Tracking 21668 as yet unmatched pairs. 3117 records in RAM.
INFO 2026-05-28 00:11:16 MarkDuplicates Read 198,000,000 records. Elapsed time: 00:10:28s. Time for last 1,000,000: 2s. Last read position: chr20:58,343,748
INFO 2026-05-28 00:11:16 MarkDuplicates Tracking 20239 as yet unmatched pairs. 1687 records in RAM.
INFO 2026-05-28 00:11:18 MarkDuplicates Read 199,000,000 records. Elapsed time: 00:10:30s. Time for last 1,000,000: 1s. Last read position: chr20:63,742,422
INFO 2026-05-28 00:11:18 MarkDuplicates Tracking 18783 as yet unmatched pairs. 231 records in RAM.
INFO 2026-05-28 00:11:20 MarkDuplicates Read 200,000,000 records. Elapsed time: 00:10:32s. Time for last 1,000,000: 1s. Last read position: chr21:25,954,626
INFO 2026-05-28 00:11:20 MarkDuplicates Tracking 17759 as yet unmatched pairs. 2179 records in RAM.
INFO 2026-05-28 00:11:22 MarkDuplicates Read 201,000,000 records. Elapsed time: 00:10:34s. Time for last 1,000,000: 2s. Last read position: chr21:44,326,020
INFO 2026-05-28 00:11:22 MarkDuplicates Tracking 16474 as yet unmatched pairs. 894 records in RAM.
INFO 2026-05-28 00:11:24 MarkDuplicates Read 202,000,000 records. Elapsed time: 00:10:37s. Time for last 1,000,000: 2s. Last read position: chr22:21,474,617
INFO 2026-05-28 00:11:24 MarkDuplicates Tracking 14888 as yet unmatched pairs. 6575 records in RAM.
INFO 2026-05-28 00:11:27 MarkDuplicates Read 203,000,000 records. Elapsed time: 00:10:39s. Time for last 1,000,000: 2s. Last read position: chr22:29,560,734
INFO 2026-05-28 00:11:27 MarkDuplicates Tracking 13404 as yet unmatched pairs. 5091 records in RAM.
INFO 2026-05-28 00:11:29 MarkDuplicates Read 204,000,000 records. Elapsed time: 00:10:41s. Time for last 1,000,000: 2s. Last read position: chr22:37,328,937
INFO 2026-05-28 00:11:29 MarkDuplicates Tracking 11934 as yet unmatched pairs. 3621 records in RAM.
INFO 2026-05-28 00:11:32 MarkDuplicates Read 205,000,000 records. Elapsed time: 00:10:44s. Time for last 1,000,000: 2s. Last read position: chr22:41,176,326
INFO 2026-05-28 00:11:32 MarkDuplicates Tracking 10710 as yet unmatched pairs. 2397 records in RAM.
INFO 2026-05-28 00:11:34 MarkDuplicates Read 206,000,000 records. Elapsed time: 00:10:47s. Time for last 1,000,000: 2s. Last read position: chr22:50,278,199
INFO 2026-05-28 00:11:34 MarkDuplicates Tracking 9205 as yet unmatched pairs. 891 records in RAM.
INFO 2026-05-28 00:11:37 MarkDuplicates Read 207,000,000 records. Elapsed time: 00:10:49s. Time for last 1,000,000: 2s. Last read position: chrX:20,162,995
INFO 2026-05-28 00:11:37 MarkDuplicates Tracking 7705 as yet unmatched pairs. 6060 records in RAM.
INFO 2026-05-28 00:11:40 MarkDuplicates Read 208,000,000 records. Elapsed time: 00:10:52s. Time for last 1,000,000: 2s. Last read position: chrX:48,896,827
INFO 2026-05-28 00:11:40 MarkDuplicates Tracking 6298 as yet unmatched pairs. 4652 records in RAM.
INFO 2026-05-28 00:11:42 MarkDuplicates Read 209,000,000 records. Elapsed time: 00:10:54s. Time for last 1,000,000: 2s. Last read position: chrX:71,294,518
INFO 2026-05-28 00:11:42 MarkDuplicates Tracking 5073 as yet unmatched pairs. 3427 records in RAM.
INFO 2026-05-28 00:11:44 MarkDuplicates Read 210,000,000 records. Elapsed time: 00:10:56s. Time for last 1,000,000: 2s. Last read position: chrX:119,539,668
INFO 2026-05-28 00:11:44 MarkDuplicates Tracking 3825 as yet unmatched pairs. 2179 records in RAM.
INFO 2026-05-28 00:11:46 MarkDuplicates Read 211,000,000 records. Elapsed time: 00:10:58s. Time for last 1,000,000: 2s. Last read position: chrX:154,353,401
INFO 2026-05-28 00:11:46 MarkDuplicates Tracking 2765 as yet unmatched pairs. 1119 records in RAM.
INFO 2026-05-28 00:11:48 MarkDuplicates Read 212,000,000 records. Elapsed time: 00:11:00s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,865
INFO 2026-05-28 00:11:48 MarkDuplicates Tracking 1096 as yet unmatched pairs. 31 records in RAM.
INFO 2026-05-28 00:11:49 MarkDuplicates Read 212742028 records. 0 pairs never matched.
INFO 2026-05-28 00:11:58 MarkDuplicates After buildSortedReadEndLists freeMemory: 37980514560; totalMemory: 62914560000; maxMemory: 63585648640
INFO 2026-05-28 00:11:58 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-05-28 00:12:04 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-05-28 00:12:37 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-05-28 00:12:55 MarkDuplicates Sorting list of duplicate records.
INFO 2026-05-28 00:13:01 MarkDuplicates After generateDuplicateIndexes freeMemory: 37300877808; totalMemory: 53250883584; maxMemory: 63585648640
INFO 2026-05-28 00:13:01 MarkDuplicates Marking 131838282 records as duplicates.
INFO 2026-05-28 00:13:01 MarkDuplicates Found 4116354 optical duplicate clusters.
INFO 2026-05-28 00:13:01 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-05-28 00:13:19 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:18s. Time for last 10,000,000: 18s. Last read position: chr1:110,017,962
INFO 2026-05-28 00:13:37 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:35s. Time for last 10,000,000: 17s. Last read position: chr1:226,392,223
INFO 2026-05-28 00:13:54 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:00:53s. Time for last 10,000,000: 17s. Last read position: chr2:156,327,881
INFO 2026-05-28 00:14:15 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:13s. Time for last 10,000,000: 20s. Last read position: chr3:42,194,855
INFO 2026-05-28 00:14:35 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:34s. Time for last 10,000,000: 20s. Last read position: chr4:39,917,125
INFO 2026-05-28 00:14:53 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:01:52s. Time for last 10,000,000: 17s. Last read position: chr5:150,402,582
INFO 2026-05-28 00:15:11 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:09s. Time for last 10,000,000: 17s. Last read position: chr6:70,528,355
INFO 2026-05-28 00:15:28 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:27s. Time for last 10,000,000: 17s. Last read position: chr7:100,607,958
INFO 2026-05-28 00:15:46 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:44s. Time for last 10,000,000: 17s. Last read position: chr8:100,718,206
INFO 2026-05-28 00:16:03 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:02s. Time for last 10,000,000: 17s. Last read position: chr9:134,045,337
INFO 2026-05-28 00:16:20 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:19s. Time for last 10,000,000: 17s. Last read position: chr11:396,645
INFO 2026-05-28 00:16:37 MarkDuplicates Written 120,000,000 records. Elapsed time: 00:03:36s. Time for last 10,000,000: 16s. Last read position: chr11:66,271,847
INFO 2026-05-28 00:16:54 MarkDuplicates Written 130,000,000 records. Elapsed time: 00:03:53s. Time for last 10,000,000: 17s. Last read position: chr12:54,281,465
INFO 2026-05-28 00:17:11 MarkDuplicates Written 140,000,000 records. Elapsed time: 00:04:10s. Time for last 10,000,000: 17s. Last read position: chr14:24,182,376
INFO 2026-05-28 00:17:29 MarkDuplicates Written 150,000,000 records. Elapsed time: 00:04:27s. Time for last 10,000,000: 17s. Last read position: chr15:78,922,083
INFO 2026-05-28 00:17:45 MarkDuplicates Written 160,000,000 records. Elapsed time: 00:04:44s. Time for last 10,000,000: 16s. Last read position: chr16:30,724,436
INFO 2026-05-28 00:18:02 MarkDuplicates Written 170,000,000 records. Elapsed time: 00:05:01s. Time for last 10,000,000: 16s. Last read position: chr17:41,763,216
INFO 2026-05-28 00:18:19 MarkDuplicates Written 180,000,000 records. Elapsed time: 00:05:17s. Time for last 10,000,000: 16s. Last read position: chr18:58,948,156
INFO 2026-05-28 00:18:36 MarkDuplicates Written 190,000,000 records. Elapsed time: 00:05:34s. Time for last 10,000,000: 16s. Last read position: chr19:42,274,434
INFO 2026-05-28 00:18:52 MarkDuplicates Written 200,000,000 records. Elapsed time: 00:05:51s. Time for last 10,000,000: 16s. Last read position: chr21:25,954,626
INFO 2026-05-28 00:19:09 MarkDuplicates Written 210,000,000 records. Elapsed time: 00:06:08s. Time for last 10,000,000: 17s. Last read position: chrX:119,539,668
INFO 2026-05-28 00:19:16 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-05-28 00:19:16 MarkDuplicates Duplicate Index cleanup.
INFO 2026-05-28 00:19:16 MarkDuplicates Getting Memory Stats.
INFO 2026-05-28 00:19:17 MarkDuplicates Before output close freeMemory: 202193160; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-05-28 00:19:17 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-05-28 00:19:17 MarkDuplicates After output close freeMemory: 104349112; totalMemory: 134217728; maxMemory: 63585648640
[Thu May 28 00:19:17 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 18.53 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory