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/77/e256a6883299ee23d850c24568eb2c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/ebb454649b9ac609ab407d41fec8e2/BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/e256a6883299ee23d850c24568eb2c/.command.run
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 BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bam --METRICS_FILE BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
07:37:20.238 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 07:37:20 GMT 2026] MarkDuplicates --INPUT BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_1.md.bam --METRICS_FILE BreastNB_FFPE_L01_RNA_01_B23LG7FLT4_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 07:37:20 GMT 2026] Executing as ?@nf-77e256a6883299ee23d850c24568eb2c-3bb9a-hh6b4 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 07:37:20 MarkDuplicates Start of doWork freeMemory: 105829272; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-06-08 07:37:20 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-06-08 07:37:20 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-06-08 07:37:25 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:03s. Time for last 1,000,000: 3s. Last read position: chr1:11,920,134
INFO 2026-06-08 07:37:25 MarkDuplicates Tracking 2044 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 07:37:27 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:05s. Time for last 1,000,000: 2s. Last read position: chr1:26,696,776
INFO 2026-06-08 07:37:27 MarkDuplicates Tracking 3910 as yet unmatched pairs. 4 records in RAM.
INFO 2026-06-08 07:37:30 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:39,429,932
INFO 2026-06-08 07:37:30 MarkDuplicates Tracking 5928 as yet unmatched pairs. 11 records in RAM.
INFO 2026-06-08 07:37:32 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 2s. Last read position: chr1:69,537,416
INFO 2026-06-08 07:37:32 MarkDuplicates Tracking 8139 as yet unmatched pairs. 3 records in RAM.
INFO 2026-06-08 07:37:35 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:13s. Time for last 1,000,000: 2s. Last read position: chr1:120,793,280
INFO 2026-06-08 07:37:35 MarkDuplicates Tracking 9778 as yet unmatched pairs. 2 records in RAM.
INFO 2026-06-08 07:37:36 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 1s. Last read position: chr1:151,428,287
INFO 2026-06-08 07:37:36 MarkDuplicates Tracking 11059 as yet unmatched pairs. 0 records in RAM.
INFO 2026-06-08 07:37:39 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:17s. Time for last 1,000,000: 2s. Last read position: chr1:161,524,586
INFO 2026-06-08 07:37:39 MarkDuplicates Tracking 12593 as yet unmatched pairs. 1 records in RAM.
INFO 2026-06-08 07:37:41 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:19s. Time for last 1,000,000: 2s. Last read position: chr1:206,478,985
INFO 2026-06-08 07:37:41 MarkDuplicates Tracking 14130 as yet unmatched pairs. 0 records in RAM.
INFO 2026-06-08 07:37:44 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:22s. Time for last 1,000,000: 2s. Last read position: chr1:236,017,197
INFO 2026-06-08 07:37:44 MarkDuplicates Tracking 16015 as yet unmatched pairs. 0 records in RAM.
INFO 2026-06-08 07:37:46 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: chr2:32,916,257
INFO 2026-06-08 07:37:46 MarkDuplicates Tracking 27853 as yet unmatched pairs. 17058 records in RAM.
INFO 2026-06-08 07:37:49 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:27s. Time for last 1,000,000: 3s. Last read position: chr2:43,225,676
INFO 2026-06-08 07:37:49 MarkDuplicates Tracking 186360 as yet unmatched pairs. 9300 records in RAM.
INFO 2026-06-08 07:37:52 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:30s. Time for last 1,000,000: 2s. Last read position: chr2:86,914,418
INFO 2026-06-08 07:37:52 MarkDuplicates Tracking 184548 as yet unmatched pairs. 7473 records in RAM.
INFO 2026-06-08 07:37:54 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:32s. Time for last 1,000,000: 2s. Last read position: chr2:117,986,017
INFO 2026-06-08 07:37:54 MarkDuplicates Tracking 183063 as yet unmatched pairs. 5966 records in RAM.
INFO 2026-06-08 07:37:56 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 2s. Last read position: chr2:188,994,233
INFO 2026-06-08 07:37:56 MarkDuplicates Tracking 181094 as yet unmatched pairs. 3982 records in RAM.
INFO 2026-06-08 07:38:00 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 3s. Last read position: chr2:218,228,882
INFO 2026-06-08 07:38:00 MarkDuplicates Tracking 179218 as yet unmatched pairs. 2102 records in RAM.
INFO 2026-06-08 07:38:02 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 2s. Last read position: chr2:241,633,854
INFO 2026-06-08 07:38:02 MarkDuplicates Tracking 177220 as yet unmatched pairs. 52 records in RAM.
INFO 2026-06-08 07:38:04 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:42s. Time for last 1,000,000: 2s. Last read position: chr3:42,637,339
INFO 2026-06-08 07:38:04 MarkDuplicates Tracking 175338 as yet unmatched pairs. 7851 records in RAM.
INFO 2026-06-08 07:38:07 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:45s. Time for last 1,000,000: 2s. Last read position: chr3:50,066,310
INFO 2026-06-08 07:38:07 MarkDuplicates Tracking 172918 as yet unmatched pairs. 5425 records in RAM.
INFO 2026-06-08 07:38:09 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:47s. Time for last 1,000,000: 2s. Last read position: chr3:111,884,107
INFO 2026-06-08 07:38:09 MarkDuplicates Tracking 170975 as yet unmatched pairs. 3469 records in RAM.
INFO 2026-06-08 07:38:11 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:49s. Time for last 1,000,000: 2s. Last read position: chr3:170,137,720
INFO 2026-06-08 07:38:11 MarkDuplicates Tracking 168623 as yet unmatched pairs. 1094 records in RAM.
INFO 2026-06-08 07:38:14 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr4:1,167,577
INFO 2026-06-08 07:38:14 MarkDuplicates Tracking 167312 as yet unmatched pairs. 4670 records in RAM.
INFO 2026-06-08 07:38:16 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr4:74,038,542
INFO 2026-06-08 07:38:16 MarkDuplicates Tracking 165293 as yet unmatched pairs. 2618 records in RAM.
INFO 2026-06-08 07:38:19 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 2s. Last read position: chr4:152,661,290
INFO 2026-06-08 07:38:19 MarkDuplicates Tracking 163420 as yet unmatched pairs. 728 records in RAM.
INFO 2026-06-08 07:38:21 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 2s. Last read position: chr5:40,633,298
INFO 2026-06-08 07:38:21 MarkDuplicates Tracking 160788 as yet unmatched pairs. 6050 records in RAM.
INFO 2026-06-08 07:38:24 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:01:02s. Time for last 1,000,000: 2s. Last read position: chr5:118,973,996
INFO 2026-06-08 07:38:24 MarkDuplicates Tracking 159173 as yet unmatched pairs. 4419 records in RAM.
INFO 2026-06-08 07:38:26 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:01:04s. Time for last 1,000,000: 2s. Last read position: chr5:150,132,700
INFO 2026-06-08 07:38:26 MarkDuplicates Tracking 157814 as yet unmatched pairs. 2838 records in RAM.
INFO 2026-06-08 07:38:29 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 2s. Last read position: chr5:179,623,133
INFO 2026-06-08 07:38:29 MarkDuplicates Tracking 155607 as yet unmatched pairs. 620 records in RAM.
INFO 2026-06-08 07:38:31 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 2s. Last read position: chr6:28,232,571
INFO 2026-06-08 07:38:31 MarkDuplicates Tracking 153489 as yet unmatched pairs. 6976 records in RAM.
INFO 2026-06-08 07:38:33 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 2s. Last read position: chr6:33,413,411
INFO 2026-06-08 07:38:33 MarkDuplicates Tracking 151771 as yet unmatched pairs. 5254 records in RAM.
INFO 2026-06-08 07:38:36 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:01:14s. Time for last 1,000,000: 2s. Last read position: chr6:73,387,193
INFO 2026-06-08 07:38:36 MarkDuplicates Tracking 149611 as yet unmatched pairs. 3075 records in RAM.
INFO 2026-06-08 07:38:39 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr6:139,373,612
INFO 2026-06-08 07:38:39 MarkDuplicates Tracking 148020 as yet unmatched pairs. 1455 records in RAM.
INFO 2026-06-08 07:38:41 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 2s. Last read position: chr7:5,199,555
INFO 2026-06-08 07:38:41 MarkDuplicates Tracking 146050 as yet unmatched pairs. 8631 records in RAM.
INFO 2026-06-08 07:38:44 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: chr7:47,808,247
INFO 2026-06-08 07:38:44 MarkDuplicates Tracking 144072 as yet unmatched pairs. 6642 records in RAM.
INFO 2026-06-08 07:38:46 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr7:77,059,227
INFO 2026-06-08 07:38:46 MarkDuplicates Tracking 142730 as yet unmatched pairs. 5290 records in RAM.
INFO 2026-06-08 07:38:48 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 2s. Last read position: chr7:100,812,731
INFO 2026-06-08 07:38:48 MarkDuplicates Tracking 140800 as yet unmatched pairs. 3354 records in RAM.
INFO 2026-06-08 07:38:50 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr7:137,513,842
INFO 2026-06-08 07:38:50 MarkDuplicates Tracking 139143 as yet unmatched pairs. 1679 records in RAM.
INFO 2026-06-08 07:38:52 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:30s. Time for last 1,000,000: 2s. Last read position: chr7:158,941,918
INFO 2026-06-08 07:38:52 MarkDuplicates Tracking 137475 as yet unmatched pairs. 5 records in RAM.
INFO 2026-06-08 07:38:54 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:32s. Time for last 1,000,000: 2s. Last read position: chr8:41,303,484
INFO 2026-06-08 07:38:54 MarkDuplicates Tracking 135377 as yet unmatched pairs. 5287 records in RAM.
INFO 2026-06-08 07:38:56 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:34s. Time for last 1,000,000: 2s. Last read position: chr8:115,414,883
INFO 2026-06-08 07:38:56 MarkDuplicates Tracking 133641 as yet unmatched pairs. 3537 records in RAM.
INFO 2026-06-08 07:38:59 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr8:143,860,825
INFO 2026-06-08 07:38:59 MarkDuplicates Tracking 132314 as yet unmatched pairs. 2186 records in RAM.
INFO 2026-06-08 07:39:00 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:38s. Time for last 1,000,000: 1s. Last read position: chr8:144,547,384
INFO 2026-06-08 07:39:00 MarkDuplicates Tracking 130239 as yet unmatched pairs. 110 records in RAM.
INFO 2026-06-08 07:39:03 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 2s. Last read position: chr9:40,040,880
INFO 2026-06-08 07:39:03 MarkDuplicates Tracking 128624 as yet unmatched pairs. 6111 records in RAM.
INFO 2026-06-08 07:39:05 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 2s. Last read position: chr9:106,926,796
INFO 2026-06-08 07:39:05 MarkDuplicates Tracking 127088 as yet unmatched pairs. 4566 records in RAM.
INFO 2026-06-08 07:39:07 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 2s. Last read position: chr9:130,626,438
INFO 2026-06-08 07:39:07 MarkDuplicates Tracking 124947 as yet unmatched pairs. 2414 records in RAM.
INFO 2026-06-08 07:39:09 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: chr9:137,253,274
INFO 2026-06-08 07:39:09 MarkDuplicates Tracking 122981 as yet unmatched pairs. 444 records in RAM.
INFO 2026-06-08 07:39:11 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 2s. Last read position: chr10:38,080,382
INFO 2026-06-08 07:39:11 MarkDuplicates Tracking 120990 as yet unmatched pairs. 4020 records in RAM.
INFO 2026-06-08 07:39:14 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:52s. Time for last 1,000,000: 2s. Last read position: chr10:77,835,737
INFO 2026-06-08 07:39:14 MarkDuplicates Tracking 119555 as yet unmatched pairs. 2571 records in RAM.
INFO 2026-06-08 07:39:16 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:54s. Time for last 1,000,000: 2s. Last read position: chr10:104,002,958
INFO 2026-06-08 07:39:16 MarkDuplicates Tracking 118171 as yet unmatched pairs. 1180 records in RAM.
INFO 2026-06-08 07:39:19 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 2s. Last read position: chr11:799,200
INFO 2026-06-08 07:39:19 MarkDuplicates Tracking 116340 as yet unmatched pairs. 11036 records in RAM.
INFO 2026-06-08 07:39:21 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 2s. Last read position: chr11:27,368,271
INFO 2026-06-08 07:39:21 MarkDuplicates Tracking 114137 as yet unmatched pairs. 8825 records in RAM.
INFO 2026-06-08 07:39:23 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr11:62,524,379
INFO 2026-06-08 07:39:23 MarkDuplicates Tracking 112354 as yet unmatched pairs. 7018 records in RAM.
INFO 2026-06-08 07:39:25 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:02:03s. Time for last 1,000,000: 2s. Last read position: chr11:65,654,679
INFO 2026-06-08 07:39:25 MarkDuplicates Tracking 110251 as yet unmatched pairs. 4915 records in RAM.
INFO 2026-06-08 07:39:27 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:02:05s. Time for last 1,000,000: 2s. Last read position: chr11:72,015,317
INFO 2026-06-08 07:39:27 MarkDuplicates Tracking 108325 as yet unmatched pairs. 2984 records in RAM.
INFO 2026-06-08 07:39:29 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:02:07s. Time for last 1,000,000: 2s. Last read position: chr11:114,064,373
INFO 2026-06-08 07:39:29 MarkDuplicates Tracking 106831 as yet unmatched pairs. 1479 records in RAM.
INFO 2026-06-08 07:39:31 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 2s. Last read position: chr12:6,561,671
INFO 2026-06-08 07:39:31 MarkDuplicates Tracking 104872 as yet unmatched pairs. 8441 records in RAM.
INFO 2026-06-08 07:39:33 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 2s. Last read position: chr12:48,776,252
INFO 2026-06-08 07:39:33 MarkDuplicates Tracking 103219 as yet unmatched pairs. 6778 records in RAM.
INFO 2026-06-08 07:39:36 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 2s. Last read position: chr12:56,164,404
INFO 2026-06-08 07:39:36 MarkDuplicates Tracking 101550 as yet unmatched pairs. 5105 records in RAM.
INFO 2026-06-08 07:39:38 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 2s. Last read position: chr12:91,157,114
INFO 2026-06-08 07:39:38 MarkDuplicates Tracking 99903 as yet unmatched pairs. 3449 records in RAM.
INFO 2026-06-08 07:39:40 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 2s. Last read position: chr12:121,819,868
INFO 2026-06-08 07:39:40 MarkDuplicates Tracking 97982 as yet unmatched pairs. 1519 records in RAM.
INFO 2026-06-08 07:39:42 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:02:20s. Time for last 1,000,000: 1s. Last read position: chr13:31,288,395
INFO 2026-06-08 07:39:42 MarkDuplicates Tracking 96088 as yet unmatched pairs. 2241 records in RAM.
INFO 2026-06-08 07:39:44 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:02:22s. Time for last 1,000,000: 1s. Last read position: chr13:113,363,834
INFO 2026-06-08 07:39:44 MarkDuplicates Tracking 93891 as yet unmatched pairs. 31 records in RAM.
INFO 2026-06-08 07:39:45 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr14:49,894,134
INFO 2026-06-08 07:39:45 MarkDuplicates Tracking 92266 as yet unmatched pairs. 3760 records in RAM.
INFO 2026-06-08 07:39:47 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 2s. Last read position: chr14:92,071,011
INFO 2026-06-08 07:39:47 MarkDuplicates Tracking 90432 as yet unmatched pairs. 1907 records in RAM.
INFO 2026-06-08 07:39:49 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 2s. Last read position: chr15:25,719,100
INFO 2026-06-08 07:39:49 MarkDuplicates Tracking 88535 as yet unmatched pairs. 5654 records in RAM.
INFO 2026-06-08 07:39:51 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: chr15:45,962,064
INFO 2026-06-08 07:39:51 MarkDuplicates Tracking 87075 as yet unmatched pairs. 4170 records in RAM.
INFO 2026-06-08 07:39:53 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 2s. Last read position: chr15:75,307,282
INFO 2026-06-08 07:39:53 MarkDuplicates Tracking 84792 as yet unmatched pairs. 1876 records in RAM.
INFO 2026-06-08 07:39:55 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 1s. Last read position: chr15:99,131,880
INFO 2026-06-08 07:39:55 MarkDuplicates Tracking 83180 as yet unmatched pairs. 247 records in RAM.
INFO 2026-06-08 07:39:58 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 2s. Last read position: chr16:2,475,528
INFO 2026-06-08 07:39:58 MarkDuplicates Tracking 80766 as yet unmatched pairs. 10005 records in RAM.
INFO 2026-06-08 07:40:00 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:38s. Time for last 1,000,000: 2s. Last read position: chr16:11,232,426
INFO 2026-06-08 07:40:00 MarkDuplicates Tracking 78841 as yet unmatched pairs. 8078 records in RAM.
INFO 2026-06-08 07:40:01 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: chr16:18,318,177
INFO 2026-06-08 07:40:01 MarkDuplicates Tracking 78023 as yet unmatched pairs. 7260 records in RAM.
INFO 2026-06-08 07:40:03 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:41s. Time for last 1,000,000: 2s. Last read position: chr16:21,836,981
INFO 2026-06-08 07:40:03 MarkDuplicates Tracking 77370 as yet unmatched pairs. 6606 records in RAM.
INFO 2026-06-08 07:40:05 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:43s. Time for last 1,000,000: 1s. Last read position: chr16:28,866,442
INFO 2026-06-08 07:40:05 MarkDuplicates Tracking 76511 as yet unmatched pairs. 5744 records in RAM.
INFO 2026-06-08 07:40:07 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:45s. Time for last 1,000,000: 1s. Last read position: chr16:30,720,919
INFO 2026-06-08 07:40:07 MarkDuplicates Tracking 75696 as yet unmatched pairs. 4929 records in RAM.
INFO 2026-06-08 07:40:09 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:47s. Time for last 1,000,000: 2s. Last read position: chr16:69,357,523
INFO 2026-06-08 07:40:09 MarkDuplicates Tracking 73311 as yet unmatched pairs. 2534 records in RAM.
INFO 2026-06-08 07:40:11 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:49s. Time for last 1,000,000: 2s. Last read position: chr16:89,561,664
INFO 2026-06-08 07:40:11 MarkDuplicates Tracking 71139 as yet unmatched pairs. 353 records in RAM.
INFO 2026-06-08 07:40:14 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:52s. Time for last 1,000,000: 2s. Last read position: chr17:7,512,793
INFO 2026-06-08 07:40:14 MarkDuplicates Tracking 68926 as yet unmatched pairs. 15753 records in RAM.
INFO 2026-06-08 07:40:16 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:54s. Time for last 1,000,000: 2s. Last read position: chr17:28,056,417
INFO 2026-06-08 07:40:16 MarkDuplicates Tracking 67408 as yet unmatched pairs. 14228 records in RAM.
INFO 2026-06-08 07:40:18 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:56s. Time for last 1,000,000: 1s. Last read position: chr17:39,717,339
INFO 2026-06-08 07:40:18 MarkDuplicates Tracking 65681 as yet unmatched pairs. 12498 records in RAM.
INFO 2026-06-08 07:40:20 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:57s. Time for last 1,000,000: 1s. Last read position: chr17:45,547,727
INFO 2026-06-08 07:40:20 MarkDuplicates Tracking 63367 as yet unmatched pairs. 10182 records in RAM.
INFO 2026-06-08 07:40:21 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:59s. Time for last 1,000,000: 1s. Last read position: chr17:50,189,241
INFO 2026-06-08 07:40:21 MarkDuplicates Tracking 62388 as yet unmatched pairs. 9200 records in RAM.
INFO 2026-06-08 07:40:22 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:03:00s. Time for last 1,000,000: 1s. Last read position: chr17:50,196,500
INFO 2026-06-08 07:40:22 MarkDuplicates Tracking 59739 as yet unmatched pairs. 6550 records in RAM.
INFO 2026-06-08 07:40:24 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:03:02s. Time for last 1,000,000: 1s. Last read position: chr17:64,895,939
INFO 2026-06-08 07:40:24 MarkDuplicates Tracking 57298 as yet unmatched pairs. 4105 records in RAM.
INFO 2026-06-08 07:40:26 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:03:04s. Time for last 1,000,000: 1s. Last read position: chr17:80,112,073
INFO 2026-06-08 07:40:26 MarkDuplicates Tracking 55035 as yet unmatched pairs. 1833 records in RAM.
INFO 2026-06-08 07:40:28 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:03:06s. Time for last 1,000,000: 2s. Last read position: chr18:15,005,523
INFO 2026-06-08 07:40:28 MarkDuplicates Tracking 52715 as yet unmatched pairs. 1419 records in RAM.
INFO 2026-06-08 07:40:30 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:03:08s. Time for last 1,000,000: 1s. Last read position: chr19:1,011,098
INFO 2026-06-08 07:40:30 MarkDuplicates Tracking 50907 as yet unmatched pairs. 15208 records in RAM.
INFO 2026-06-08 07:40:31 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:03:09s. Time for last 1,000,000: 1s. Last read position: chr19:5,690,507
INFO 2026-06-08 07:40:31 MarkDuplicates Tracking 48856 as yet unmatched pairs. 13151 records in RAM.
INFO 2026-06-08 07:40:33 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:03:11s. Time for last 1,000,000: 1s. Last read position: chr19:12,797,141
INFO 2026-06-08 07:40:33 MarkDuplicates Tracking 46854 as yet unmatched pairs. 11148 records in RAM.
INFO 2026-06-08 07:40:35 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:03:13s. Time for last 1,000,000: 2s. Last read position: chr19:18,155,921
INFO 2026-06-08 07:40:35 MarkDuplicates Tracking 44808 as yet unmatched pairs. 9087 records in RAM.
INFO 2026-06-08 07:40:37 MarkDuplicates Read 89,000,000 records. Elapsed time: 00:03:15s. Time for last 1,000,000: 1s. Last read position: chr19:39,407,944
INFO 2026-06-08 07:40:37 MarkDuplicates Tracking 42306 as yet unmatched pairs. 6580 records in RAM.
INFO 2026-06-08 07:40:39 MarkDuplicates Read 90,000,000 records. Elapsed time: 00:03:17s. Time for last 1,000,000: 2s. Last read position: chr19:45,179,856
INFO 2026-06-08 07:40:39 MarkDuplicates Tracking 40553 as yet unmatched pairs. 4792 records in RAM.
INFO 2026-06-08 07:40:41 MarkDuplicates Read 91,000,000 records. Elapsed time: 00:03:19s. Time for last 1,000,000: 1s. Last read position: chr19:49,616,039
INFO 2026-06-08 07:40:41 MarkDuplicates Tracking 38570 as yet unmatched pairs. 2804 records in RAM.
INFO 2026-06-08 07:40:43 MarkDuplicates Read 92,000,000 records. Elapsed time: 00:03:21s. Time for last 1,000,000: 2s. Last read position: chr19:57,477,322
INFO 2026-06-08 07:40:43 MarkDuplicates Tracking 36234 as yet unmatched pairs. 467 records in RAM.
INFO 2026-06-08 07:40:45 MarkDuplicates Read 93,000,000 records. Elapsed time: 00:03:23s. Time for last 1,000,000: 1s. Last read position: chr20:19,799,723
INFO 2026-06-08 07:40:45 MarkDuplicates Tracking 34471 as yet unmatched pairs. 3676 records in RAM.
INFO 2026-06-08 07:40:46 MarkDuplicates Read 94,000,000 records. Elapsed time: 00:03:24s. Time for last 1,000,000: 1s. Last read position: chr20:49,224,968
INFO 2026-06-08 07:40:46 MarkDuplicates Tracking 32407 as yet unmatched pairs. 1608 records in RAM.
INFO 2026-06-08 07:40:48 MarkDuplicates Read 95,000,000 records. Elapsed time: 00:03:26s. Time for last 1,000,000: 1s. Last read position: chr21:8,210,385
INFO 2026-06-08 07:40:48 MarkDuplicates Tracking 30683 as yet unmatched pairs. 9323 records in RAM.
INFO 2026-06-08 07:40:49 MarkDuplicates Read 96,000,000 records. Elapsed time: 00:03:27s. Time for last 1,000,000: 1s. Last read position: chr21:8,216,852
INFO 2026-06-08 07:40:49 MarkDuplicates Tracking 29465 as yet unmatched pairs. 8090 records in RAM.
INFO 2026-06-08 07:40:51 MarkDuplicates Read 97,000,000 records. Elapsed time: 00:03:29s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,913
INFO 2026-06-08 07:40:51 MarkDuplicates Tracking 28572 as yet unmatched pairs. 7193 records in RAM.
INFO 2026-06-08 07:40:52 MarkDuplicates Read 98,000,000 records. Elapsed time: 00:03:30s. Time for last 1,000,000: 1s. Last read position: chr21:8,390,749
INFO 2026-06-08 07:40:52 MarkDuplicates Tracking 28523 as yet unmatched pairs. 7142 records in RAM.
INFO 2026-06-08 07:40:54 MarkDuplicates Read 99,000,000 records. Elapsed time: 00:03:32s. Time for last 1,000,000: 1s. Last read position: chr21:8,399,947
INFO 2026-06-08 07:40:54 MarkDuplicates Tracking 27082 as yet unmatched pairs. 5696 records in RAM.
INFO 2026-06-08 07:40:55 MarkDuplicates Read 100,000,000 records. Elapsed time: 00:03:33s. Time for last 1,000,000: 1s. Last read position: chr21:8,441,960
INFO 2026-06-08 07:40:55 MarkDuplicates Tracking 25175 as yet unmatched pairs. 3776 records in RAM.
INFO 2026-06-08 07:40:57 MarkDuplicates Read 101,000,000 records. Elapsed time: 00:03:35s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,115
INFO 2026-06-08 07:40:57 MarkDuplicates Tracking 24289 as yet unmatched pairs. 2888 records in RAM.
INFO 2026-06-08 07:40:58 MarkDuplicates Read 102,000,000 records. Elapsed time: 00:03:36s. Time for last 1,000,000: 1s. Last read position: chr21:33,555,064
INFO 2026-06-08 07:40:58 MarkDuplicates Tracking 23338 as yet unmatched pairs. 1936 records in RAM.
INFO 2026-06-08 07:41:00 MarkDuplicates Read 103,000,000 records. Elapsed time: 00:03:38s. Time for last 1,000,000: 1s. Last read position: chr22:17,864,944
INFO 2026-06-08 07:41:00 MarkDuplicates Tracking 21239 as yet unmatched pairs. 5623 records in RAM.
INFO 2026-06-08 07:41:02 MarkDuplicates Read 104,000,000 records. Elapsed time: 00:03:40s. Time for last 1,000,000: 1s. Last read position: chr22:31,125,270
INFO 2026-06-08 07:41:02 MarkDuplicates Tracking 19410 as yet unmatched pairs. 3792 records in RAM.
INFO 2026-06-08 07:41:04 MarkDuplicates Read 105,000,000 records. Elapsed time: 00:03:42s. Time for last 1,000,000: 2s. Last read position: chr22:42,211,205
INFO 2026-06-08 07:41:04 MarkDuplicates Tracking 17109 as yet unmatched pairs. 1489 records in RAM.
INFO 2026-06-08 07:41:07 MarkDuplicates Read 106,000,000 records. Elapsed time: 00:03:45s. Time for last 1,000,000: 2s. Last read position: chrX:31,147,423
INFO 2026-06-08 07:41:07 MarkDuplicates Tracking 14813 as yet unmatched pairs. 3239 records in RAM.
INFO 2026-06-08 07:41:09 MarkDuplicates Read 107,000,000 records. Elapsed time: 00:03:47s. Time for last 1,000,000: 2s. Last read position: chrX:77,951,770
INFO 2026-06-08 07:41:09 MarkDuplicates Tracking 13134 as yet unmatched pairs. 1552 records in RAM.
INFO 2026-06-08 07:41:11 MarkDuplicates Read 108,000,000 records. Elapsed time: 00:03:49s. Time for last 1,000,000: 2s. Last read position: chrY:7,606,334
INFO 2026-06-08 07:41:11 MarkDuplicates Tracking 11582 as yet unmatched pairs. 57 records in RAM.
INFO 2026-06-08 07:41:13 MarkDuplicates Read 109,000,000 records. Elapsed time: 00:03:51s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,195
INFO 2026-06-08 07:41:13 MarkDuplicates Tracking 11288 as yet unmatched pairs. 1384 records in RAM.
INFO 2026-06-08 07:41:14 MarkDuplicates Read 110,000,000 records. Elapsed time: 00:03:52s. Time for last 1,000,000: 1s. Last read position: GL000220.1:116,776
INFO 2026-06-08 07:41:14 MarkDuplicates Tracking 10001 as yet unmatched pairs. 97 records in RAM.
INFO 2026-06-08 07:41:16 MarkDuplicates Read 111,000,000 records. Elapsed time: 00:03:54s. Time for last 1,000,000: 1s. Last read position: GL000220.1:158,158
INFO 2026-06-08 07:41:16 MarkDuplicates Tracking 9986 as yet unmatched pairs. 82 records in RAM.
INFO 2026-06-08 07:41:17 MarkDuplicates Read 112,000,000 records. Elapsed time: 00:03:55s. Time for last 1,000,000: 1s. Last read position: GL000220.1:160,692
INFO 2026-06-08 07:41:17 MarkDuplicates Tracking 9918 as yet unmatched pairs. 14 records in RAM.
INFO 2026-06-08 07:41:19 MarkDuplicates Read 113,000,000 records. Elapsed time: 00:03:57s. Time for last 1,000,000: 1s. Last read position: KI270733.1:131,020
INFO 2026-06-08 07:41:19 MarkDuplicates Tracking 5604 as yet unmatched pairs. 5562 records in RAM.
INFO 2026-06-08 07:41:21 MarkDuplicates Read 114,000,000 records. Elapsed time: 00:03:59s. Time for last 1,000,000: 2s. Last read position: KI270733.1:133,174
INFO 2026-06-08 07:41:21 MarkDuplicates Tracking 1428 as yet unmatched pairs. 1386 records in RAM.
INFO 2026-06-08 07:41:23 MarkDuplicates Read 115,000,000 records. Elapsed time: 00:04:01s. Time for last 1,000,000: 1s. Last read position: KI270733.1:176,077
INFO 2026-06-08 07:41:23 MarkDuplicates Tracking 255 as yet unmatched pairs. 213 records in RAM.
INFO 2026-06-08 07:41:24 MarkDuplicates Read 116,000,000 records. Elapsed time: 00:04:02s. Time for last 1,000,000: 1s. Last read position: KI270733.1:177,455
INFO 2026-06-08 07:41:24 MarkDuplicates Tracking 147 as yet unmatched pairs. 105 records in RAM.
INFO 2026-06-08 07:41:26 MarkDuplicates Read 116897765 records. 0 pairs never matched.
INFO 2026-06-08 07:41:32 MarkDuplicates After buildSortedReadEndLists freeMemory: 31176081392; totalMemory: 44526731264; maxMemory: 63585648640
INFO 2026-06-08 07:41:32 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-06-08 07:41:39 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-06-08 07:41:59 OpticalDuplicateFinder Large duplicate set. size = 1083
INFO 2026-06-08 07:41:59 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-20,065
INFO 2026-06-08 07:41:59 OpticalDuplicateFinder Large duplicate set. size = 1302
INFO 2026-06-08 07:41:59 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:32,761
INFO 2026-06-08 07:41:59 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-06-08 07:42:06 MarkDuplicates Sorting list of duplicate records.
INFO 2026-06-08 07:42:10 MarkDuplicates After generateDuplicateIndexes freeMemory: 28576650168; totalMemory: 44526731264; maxMemory: 63585648640
INFO 2026-06-08 07:42:10 MarkDuplicates Marking 79516006 records as duplicates.
INFO 2026-06-08 07:42:10 MarkDuplicates Found 1936179 optical duplicate clusters.
INFO 2026-06-08 07:42:10 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-06-08 07:42:30 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:20s. Time for last 10,000,000: 20s. Last read position: chr2:32,916,257
INFO 2026-06-08 07:42:52 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:42s. Time for last 10,000,000: 21s. Last read position: chr3:170,137,720
INFO 2026-06-08 07:43:13 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:02s. Time for last 10,000,000: 20s. Last read position: chr6:73,387,193
INFO 2026-06-08 07:43:33 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:22s. Time for last 10,000,000: 20s. Last read position: chr8:143,860,825
INFO 2026-06-08 07:43:51 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:01:41s. Time for last 10,000,000: 18s. Last read position: chr11:27,368,271
INFO 2026-06-08 07:44:10 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:00s. Time for last 10,000,000: 18s. Last read position: chr13:31,288,395
INFO 2026-06-08 07:44:30 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:02:19s. Time for last 10,000,000: 19s. Last read position: chr16:18,318,177
INFO 2026-06-08 07:44:50 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:02:39s. Time for last 10,000,000: 20s. Last read position: chr17:50,189,241
INFO 2026-06-08 07:45:07 MarkDuplicates Written 90,000,000 records. Elapsed time: 00:02:57s. Time for last 10,000,000: 17s. Last read position: chr19:45,179,856
INFO 2026-06-08 07:45:26 MarkDuplicates Written 100,000,000 records. Elapsed time: 00:03:15s. Time for last 10,000,000: 18s. Last read position: chr21:8,441,960
INFO 2026-06-08 07:45:44 MarkDuplicates Written 110,000,000 records. Elapsed time: 00:03:34s. Time for last 10,000,000: 18s. Last read position: GL000220.1:116,776
INFO 2026-06-08 07:46:00 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-06-08 07:46:00 MarkDuplicates Duplicate Index cleanup.
INFO 2026-06-08 07:46:00 MarkDuplicates Getting Memory Stats.
INFO 2026-06-08 07:46:00 MarkDuplicates Before output close freeMemory: 201825944; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-06-08 07:46:00 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-06-08 07:46:00 MarkDuplicates After output close freeMemory: 104275648; totalMemory: 134217728; maxMemory: 63585648640
[Mon Jun 08 07:46:00 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 8.68 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory