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/91/123bb3ed29490113429b0c59ac6384/.command.sh
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_genome.fa.fai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/123bb3ed29490113429b0c59ac6384/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/79/71117a58f0b32aa82ed8ea882f6136/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)
Using GATK jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx60620M -XX:-UsePerfData -XX:ParallelGCThreads=2 -jar /usr/local/share/gatk4-4.4.0.0-0/gatk-package-4.4.0.0-local.jar MarkDuplicates --INPUT BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bam --METRICS_FILE BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bam.metrics --TMP_DIR . --CREATE_INDEX true --REFERENCE_SEQUENCE ref_genome.fa -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT
20:14:08.023 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 20:14:08 GMT 2026] MarkDuplicates --INPUT BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam --OUTPUT BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.md.bam --METRICS_FILE BreastNP_FFPE_L04_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
[Thu May 28 20:14:08 GMT 2026] Executing as ?@nf-91123bb3ed29490113429b0c59ac6384-e2c3b-6nkv8 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 20:14:08 MarkDuplicates Start of doWork freeMemory: 105827112; totalMemory: 134217728; maxMemory: 63585648640
INFO 2026-05-28 20:14:08 MarkDuplicates Reading input file and constructing read end information.
INFO 2026-05-28 20:14:08 MarkDuplicates Will retain up to 230382784 data points before spilling to disk.
INFO 2026-05-28 20:14:11 MarkDuplicates Read 1,000,000 records. Elapsed time: 00:00:02s. Time for last 1,000,000: 2s. Last read position: chr1:17,687,621
INFO 2026-05-28 20:14:11 MarkDuplicates Tracking 1646 as yet unmatched pairs. 4 records in RAM.
INFO 2026-05-28 20:14:14 MarkDuplicates Read 2,000,000 records. Elapsed time: 00:00:04s. Time for last 1,000,000: 2s. Last read position: chr1:35,192,514
INFO 2026-05-28 20:14:14 MarkDuplicates Tracking 3396 as yet unmatched pairs. 3 records in RAM.
INFO 2026-05-28 20:14:15 MarkDuplicates Read 3,000,000 records. Elapsed time: 00:00:06s. Time for last 1,000,000: 1s. Last read position: chr1:77,129,495
INFO 2026-05-28 20:14:15 MarkDuplicates Tracking 5564 as yet unmatched pairs. 5 records in RAM.
INFO 2026-05-28 20:14:18 MarkDuplicates Read 4,000,000 records. Elapsed time: 00:00:08s. Time for last 1,000,000: 2s. Last read position: chr1:148,615,701
INFO 2026-05-28 20:14:18 MarkDuplicates Tracking 7240 as yet unmatched pairs. 4 records in RAM.
INFO 2026-05-28 20:14:19 MarkDuplicates Read 5,000,000 records. Elapsed time: 00:00:10s. Time for last 1,000,000: 1s. Last read position: chr1:156,670,333
INFO 2026-05-28 20:14:19 MarkDuplicates Tracking 8681 as yet unmatched pairs. 20 records in RAM.
INFO 2026-05-28 20:14:21 MarkDuplicates Read 6,000,000 records. Elapsed time: 00:00:12s. Time for last 1,000,000: 1s. Last read position: chr1:207,886,756
INFO 2026-05-28 20:14:21 MarkDuplicates Tracking 10486 as yet unmatched pairs. 190 records in RAM.
INFO 2026-05-28 20:14:23 MarkDuplicates Read 7,000,000 records. Elapsed time: 00:00:14s. Time for last 1,000,000: 2s. Last read position: chr2:24,683,110
INFO 2026-05-28 20:14:23 MarkDuplicates Tracking 12120 as yet unmatched pairs. 11845 records in RAM.
INFO 2026-05-28 20:14:26 MarkDuplicates Read 8,000,000 records. Elapsed time: 00:00:16s. Time for last 1,000,000: 2s. Last read position: chr2:43,260,074
INFO 2026-05-28 20:14:26 MarkDuplicates Tracking 118546 as yet unmatched pairs. 5613 records in RAM.
INFO 2026-05-28 20:14:27 MarkDuplicates Read 9,000,000 records. Elapsed time: 00:00:18s. Time for last 1,000,000: 1s. Last read position: chr2:101,859,736
INFO 2026-05-28 20:14:27 MarkDuplicates Tracking 116999 as yet unmatched pairs. 4030 records in RAM.
INFO 2026-05-28 20:14:29 MarkDuplicates Read 10,000,000 records. Elapsed time: 00:00:20s. Time for last 1,000,000: 1s. Last read position: chr2:188,994,548
INFO 2026-05-28 20:14:29 MarkDuplicates Tracking 115673 as yet unmatched pairs. 2680 records in RAM.
INFO 2026-05-28 20:14:31 MarkDuplicates Read 11,000,000 records. Elapsed time: 00:00:21s. Time for last 1,000,000: 1s. Last read position: chr2:219,558,386
INFO 2026-05-28 20:14:31 MarkDuplicates Tracking 113971 as yet unmatched pairs. 973 records in RAM.
INFO 2026-05-28 20:14:33 MarkDuplicates Read 12,000,000 records. Elapsed time: 00:00:24s. Time for last 1,000,000: 2s. Last read position: chr3:30,963,602
INFO 2026-05-28 20:14:33 MarkDuplicates Tracking 112595 as yet unmatched pairs. 3947 records in RAM.
INFO 2026-05-28 20:14:35 MarkDuplicates Read 13,000,000 records. Elapsed time: 00:00:26s. Time for last 1,000,000: 1s. Last read position: chr3:52,480,337
INFO 2026-05-28 20:14:35 MarkDuplicates Tracking 111293 as yet unmatched pairs. 2628 records in RAM.
INFO 2026-05-28 20:14:37 MarkDuplicates Read 14,000,000 records. Elapsed time: 00:00:28s. Time for last 1,000,000: 1s. Last read position: chr3:133,586,626
INFO 2026-05-28 20:14:37 MarkDuplicates Tracking 109743 as yet unmatched pairs. 1047 records in RAM.
INFO 2026-05-28 20:14:39 MarkDuplicates Read 15,000,000 records. Elapsed time: 00:00:29s. Time for last 1,000,000: 1s. Last read position: chr4:1,823,023
INFO 2026-05-28 20:14:39 MarkDuplicates Tracking 108374 as yet unmatched pairs. 2586 records in RAM.
INFO 2026-05-28 20:14:40 MarkDuplicates Read 16,000,000 records. Elapsed time: 00:00:31s. Time for last 1,000,000: 1s. Last read position: chr4:104,494,739
INFO 2026-05-28 20:14:40 MarkDuplicates Tracking 106922 as yet unmatched pairs. 1068 records in RAM.
INFO 2026-05-28 20:14:42 MarkDuplicates Read 17,000,000 records. Elapsed time: 00:00:33s. Time for last 1,000,000: 1s. Last read position: chr5:31,526,590
INFO 2026-05-28 20:14:42 MarkDuplicates Tracking 105322 as yet unmatched pairs. 4746 records in RAM.
INFO 2026-05-28 20:14:44 MarkDuplicates Read 18,000,000 records. Elapsed time: 00:00:34s. Time for last 1,000,000: 1s. Last read position: chr5:136,054,800
INFO 2026-05-28 20:14:44 MarkDuplicates Tracking 103666 as yet unmatched pairs. 3071 records in RAM.
INFO 2026-05-28 20:14:46 MarkDuplicates Read 19,000,000 records. Elapsed time: 00:00:36s. Time for last 1,000,000: 1s. Last read position: chr5:157,744,023
INFO 2026-05-28 20:14:46 MarkDuplicates Tracking 102248 as yet unmatched pairs. 1203 records in RAM.
INFO 2026-05-28 20:14:47 MarkDuplicates Read 20,000,000 records. Elapsed time: 00:00:38s. Time for last 1,000,000: 1s. Last read position: chr6:15,334,513
INFO 2026-05-28 20:14:47 MarkDuplicates Tracking 100513 as yet unmatched pairs. 5599 records in RAM.
INFO 2026-05-28 20:14:49 MarkDuplicates Read 21,000,000 records. Elapsed time: 00:00:40s. Time for last 1,000,000: 1s. Last read position: chr6:32,081,604
INFO 2026-05-28 20:14:49 MarkDuplicates Tracking 98792 as yet unmatched pairs. 3834 records in RAM.
INFO 2026-05-28 20:14:51 MarkDuplicates Read 22,000,000 records. Elapsed time: 00:00:41s. Time for last 1,000,000: 1s. Last read position: chr6:79,203,580
INFO 2026-05-28 20:14:51 MarkDuplicates Tracking 97310 as yet unmatched pairs. 2344 records in RAM.
INFO 2026-05-28 20:14:53 MarkDuplicates Read 23,000,000 records. Elapsed time: 00:00:43s. Time for last 1,000,000: 1s. Last read position: chr6:151,353,644
INFO 2026-05-28 20:14:53 MarkDuplicates Tracking 95710 as yet unmatched pairs. 724 records in RAM.
INFO 2026-05-28 20:14:55 MarkDuplicates Read 24,000,000 records. Elapsed time: 00:00:46s. Time for last 1,000,000: 2s. Last read position: chr7:23,507,440
INFO 2026-05-28 20:14:55 MarkDuplicates Tracking 93585 as yet unmatched pairs. 4976 records in RAM.
INFO 2026-05-28 20:14:57 MarkDuplicates Read 25,000,000 records. Elapsed time: 00:00:48s. Time for last 1,000,000: 2s. Last read position: chr7:75,557,706
INFO 2026-05-28 20:14:57 MarkDuplicates Tracking 92052 as yet unmatched pairs. 3423 records in RAM.
INFO 2026-05-28 20:14:59 MarkDuplicates Read 26,000,000 records. Elapsed time: 00:00:50s. Time for last 1,000,000: 1s. Last read position: chr7:102,654,713
INFO 2026-05-28 20:14:59 MarkDuplicates Tracking 90565 as yet unmatched pairs. 1918 records in RAM.
INFO 2026-05-28 20:15:02 MarkDuplicates Read 27,000,000 records. Elapsed time: 00:00:52s. Time for last 1,000,000: 2s. Last read position: chr7:152,154,034
INFO 2026-05-28 20:15:02 MarkDuplicates Tracking 88835 as yet unmatched pairs. 160 records in RAM.
INFO 2026-05-28 20:15:03 MarkDuplicates Read 28,000,000 records. Elapsed time: 00:00:54s. Time for last 1,000,000: 1s. Last read position: chr8:41,934,447
INFO 2026-05-28 20:15:03 MarkDuplicates Tracking 87374 as yet unmatched pairs. 2713 records in RAM.
INFO 2026-05-28 20:15:05 MarkDuplicates Read 29,000,000 records. Elapsed time: 00:00:55s. Time for last 1,000,000: 1s. Last read position: chr8:127,740,760
INFO 2026-05-28 20:15:05 MarkDuplicates Tracking 85767 as yet unmatched pairs. 1096 records in RAM.
INFO 2026-05-28 20:15:07 MarkDuplicates Read 30,000,000 records. Elapsed time: 00:00:57s. Time for last 1,000,000: 1s. Last read position: chr9:14,116,232
INFO 2026-05-28 20:15:07 MarkDuplicates Tracking 84442 as yet unmatched pairs. 4358 records in RAM.
INFO 2026-05-28 20:15:09 MarkDuplicates Read 31,000,000 records. Elapsed time: 00:00:59s. Time for last 1,000,000: 1s. Last read position: chr9:96,937,240
INFO 2026-05-28 20:15:09 MarkDuplicates Tracking 83245 as yet unmatched pairs. 2965 records in RAM.
INFO 2026-05-28 20:15:10 MarkDuplicates Read 32,000,000 records. Elapsed time: 00:01:01s. Time for last 1,000,000: 1s. Last read position: chr9:131,468,679
INFO 2026-05-28 20:15:10 MarkDuplicates Tracking 81660 as yet unmatched pairs. 1370 records in RAM.
INFO 2026-05-28 20:15:12 MarkDuplicates Read 33,000,000 records. Elapsed time: 00:01:03s. Time for last 1,000,000: 2s. Last read position: chr10:17,359,539
INFO 2026-05-28 20:15:12 MarkDuplicates Tracking 79941 as yet unmatched pairs. 3011 records in RAM.
INFO 2026-05-28 20:15:14 MarkDuplicates Read 34,000,000 records. Elapsed time: 00:01:05s. Time for last 1,000,000: 2s. Last read position: chr10:77,809,708
INFO 2026-05-28 20:15:14 MarkDuplicates Tracking 78700 as yet unmatched pairs. 1749 records in RAM.
INFO 2026-05-28 20:15:16 MarkDuplicates Read 35,000,000 records. Elapsed time: 00:01:07s. Time for last 1,000,000: 1s. Last read position: chr10:125,838,278
INFO 2026-05-28 20:15:16 MarkDuplicates Tracking 77180 as yet unmatched pairs. 183 records in RAM.
INFO 2026-05-28 20:15:18 MarkDuplicates Read 36,000,000 records. Elapsed time: 00:01:09s. Time for last 1,000,000: 1s. Last read position: chr11:14,643,986
INFO 2026-05-28 20:15:18 MarkDuplicates Tracking 75510 as yet unmatched pairs. 5721 records in RAM.
INFO 2026-05-28 20:15:21 MarkDuplicates Read 37,000,000 records. Elapsed time: 00:01:11s. Time for last 1,000,000: 2s. Last read position: chr11:62,528,929
INFO 2026-05-28 20:15:21 MarkDuplicates Tracking 74114 as yet unmatched pairs. 4276 records in RAM.
INFO 2026-05-28 20:15:23 MarkDuplicates Read 38,000,000 records. Elapsed time: 00:01:13s. Time for last 1,000,000: 2s. Last read position: chr11:68,312,724
INFO 2026-05-28 20:15:23 MarkDuplicates Tracking 72513 as yet unmatched pairs. 2668 records in RAM.
INFO 2026-05-28 20:15:24 MarkDuplicates Read 39,000,000 records. Elapsed time: 00:01:15s. Time for last 1,000,000: 1s. Last read position: chr11:114,064,077
INFO 2026-05-28 20:15:24 MarkDuplicates Tracking 70853 as yet unmatched pairs. 994 records in RAM.
INFO 2026-05-28 20:15:27 MarkDuplicates Read 40,000,000 records. Elapsed time: 00:01:17s. Time for last 1,000,000: 2s. Last read position: chr12:8,224,718
INFO 2026-05-28 20:15:27 MarkDuplicates Tracking 69141 as yet unmatched pairs. 5486 records in RAM.
INFO 2026-05-28 20:15:28 MarkDuplicates Read 41,000,000 records. Elapsed time: 00:01:19s. Time for last 1,000,000: 1s. Last read position: chr12:52,520,045
INFO 2026-05-28 20:15:28 MarkDuplicates Tracking 67513 as yet unmatched pairs. 3855 records in RAM.
INFO 2026-05-28 20:15:30 MarkDuplicates Read 42,000,000 records. Elapsed time: 00:01:20s. Time for last 1,000,000: 1s. Last read position: chr12:66,152,286
INFO 2026-05-28 20:15:30 MarkDuplicates Tracking 66104 as yet unmatched pairs. 2440 records in RAM.
INFO 2026-05-28 20:15:32 MarkDuplicates Read 43,000,000 records. Elapsed time: 00:01:22s. Time for last 1,000,000: 2s. Last read position: chr12:122,133,452
INFO 2026-05-28 20:15:32 MarkDuplicates Tracking 64698 as yet unmatched pairs. 1016 records in RAM.
INFO 2026-05-28 20:15:34 MarkDuplicates Read 44,000,000 records. Elapsed time: 00:01:24s. Time for last 1,000,000: 1s. Last read position: chr13:50,843,495
INFO 2026-05-28 20:15:34 MarkDuplicates Tracking 63180 as yet unmatched pairs. 789 records in RAM.
INFO 2026-05-28 20:15:35 MarkDuplicates Read 45,000,000 records. Elapsed time: 00:01:26s. Time for last 1,000,000: 1s. Last read position: chr14:39,181,488
INFO 2026-05-28 20:15:35 MarkDuplicates Tracking 61639 as yet unmatched pairs. 2472 records in RAM.
INFO 2026-05-28 20:15:37 MarkDuplicates Read 46,000,000 records. Elapsed time: 00:01:28s. Time for last 1,000,000: 1s. Last read position: chr14:95,260,818
INFO 2026-05-28 20:15:37 MarkDuplicates Tracking 60154 as yet unmatched pairs. 961 records in RAM.
INFO 2026-05-28 20:15:39 MarkDuplicates Read 47,000,000 records. Elapsed time: 00:01:29s. Time for last 1,000,000: 1s. Last read position: chr15:42,746,053
INFO 2026-05-28 20:15:39 MarkDuplicates Tracking 58580 as yet unmatched pairs. 2542 records in RAM.
INFO 2026-05-28 20:15:40 MarkDuplicates Read 48,000,000 records. Elapsed time: 00:01:31s. Time for last 1,000,000: 1s. Last read position: chr15:77,467,154
INFO 2026-05-28 20:15:40 MarkDuplicates Tracking 56970 as yet unmatched pairs. 920 records in RAM.
INFO 2026-05-28 20:15:43 MarkDuplicates Read 49,000,000 records. Elapsed time: 00:01:33s. Time for last 1,000,000: 2s. Last read position: chr16:2,093,614
INFO 2026-05-28 20:15:43 MarkDuplicates Tracking 55258 as yet unmatched pairs. 5861 records in RAM.
INFO 2026-05-28 20:15:45 MarkDuplicates Read 50,000,000 records. Elapsed time: 00:01:35s. Time for last 1,000,000: 1s. Last read position: chr16:15,127,728
INFO 2026-05-28 20:15:45 MarkDuplicates Tracking 54147 as yet unmatched pairs. 4745 records in RAM.
INFO 2026-05-28 20:15:47 MarkDuplicates Read 51,000,000 records. Elapsed time: 00:01:37s. Time for last 1,000,000: 2s. Last read position: chr16:22,523,832
INFO 2026-05-28 20:15:47 MarkDuplicates Tracking 53436 as yet unmatched pairs. 4029 records in RAM.
INFO 2026-05-28 20:15:49 MarkDuplicates Read 52,000,000 records. Elapsed time: 00:01:39s. Time for last 1,000,000: 2s. Last read position: chr16:30,729,220
INFO 2026-05-28 20:15:49 MarkDuplicates Tracking 52253 as yet unmatched pairs. 2839 records in RAM.
INFO 2026-05-28 20:15:51 MarkDuplicates Read 53,000,000 records. Elapsed time: 00:01:41s. Time for last 1,000,000: 1s. Last read position: chr16:83,161,630
INFO 2026-05-28 20:15:51 MarkDuplicates Tracking 50244 as yet unmatched pairs. 788 records in RAM.
INFO 2026-05-28 20:15:53 MarkDuplicates Read 54,000,000 records. Elapsed time: 00:01:43s. Time for last 1,000,000: 2s. Last read position: chr17:7,384,700
INFO 2026-05-28 20:15:53 MarkDuplicates Tracking 48516 as yet unmatched pairs. 10288 records in RAM.
INFO 2026-05-28 20:15:55 MarkDuplicates Read 55,000,000 records. Elapsed time: 00:01:45s. Time for last 1,000,000: 1s. Last read position: chr17:28,701,573
INFO 2026-05-28 20:15:55 MarkDuplicates Tracking 47336 as yet unmatched pairs. 9103 records in RAM.
INFO 2026-05-28 20:15:57 MarkDuplicates Read 56,000,000 records. Elapsed time: 00:01:47s. Time for last 1,000,000: 2s. Last read position: chr17:42,300,129
INFO 2026-05-28 20:15:57 MarkDuplicates Tracking 45795 as yet unmatched pairs. 7556 records in RAM.
INFO 2026-05-28 20:15:59 MarkDuplicates Read 57,000,000 records. Elapsed time: 00:01:49s. Time for last 1,000,000: 1s. Last read position: chr17:50,187,967
INFO 2026-05-28 20:15:59 MarkDuplicates Tracking 44812 as yet unmatched pairs. 6570 records in RAM.
INFO 2026-05-28 20:16:00 MarkDuplicates Read 58,000,000 records. Elapsed time: 00:01:51s. Time for last 1,000,000: 1s. Last read position: chr17:50,194,754
INFO 2026-05-28 20:16:00 MarkDuplicates Tracking 43030 as yet unmatched pairs. 4788 records in RAM.
INFO 2026-05-28 20:16:03 MarkDuplicates Read 59,000,000 records. Elapsed time: 00:01:53s. Time for last 1,000,000: 2s. Last read position: chr17:62,573,302
INFO 2026-05-28 20:16:03 MarkDuplicates Tracking 40784 as yet unmatched pairs. 2538 records in RAM.
INFO 2026-05-28 20:16:05 MarkDuplicates Read 60,000,000 records. Elapsed time: 00:01:55s. Time for last 1,000,000: 2s. Last read position: chr17:81,512,113
INFO 2026-05-28 20:16:05 MarkDuplicates Tracking 38920 as yet unmatched pairs. 666 records in RAM.
INFO 2026-05-28 20:16:07 MarkDuplicates Read 61,000,000 records. Elapsed time: 00:01:57s. Time for last 1,000,000: 1s. Last read position: chr18:77,017,032
INFO 2026-05-28 20:16:07 MarkDuplicates Tracking 37215 as yet unmatched pairs. 68 records in RAM.
INFO 2026-05-28 20:16:08 MarkDuplicates Read 62,000,000 records. Elapsed time: 00:01:59s. Time for last 1,000,000: 1s. Last read position: chr19:6,709,826
INFO 2026-05-28 20:16:08 MarkDuplicates Tracking 35462 as yet unmatched pairs. 8560 records in RAM.
INFO 2026-05-28 20:16:10 MarkDuplicates Read 63,000,000 records. Elapsed time: 00:02:01s. Time for last 1,000,000: 2s. Last read position: chr19:15,244,267
INFO 2026-05-28 20:16:10 MarkDuplicates Tracking 34034 as yet unmatched pairs. 7124 records in RAM.
INFO 2026-05-28 20:16:12 MarkDuplicates Read 64,000,000 records. Elapsed time: 00:02:02s. Time for last 1,000,000: 1s. Last read position: chr19:35,269,140
INFO 2026-05-28 20:16:12 MarkDuplicates Tracking 31650 as yet unmatched pairs. 4721 records in RAM.
INFO 2026-05-28 20:16:14 MarkDuplicates Read 65,000,000 records. Elapsed time: 00:02:04s. Time for last 1,000,000: 1s. Last read position: chr19:42,287,204
INFO 2026-05-28 20:16:14 MarkDuplicates Tracking 30055 as yet unmatched pairs. 3119 records in RAM.
INFO 2026-05-28 20:16:15 MarkDuplicates Read 66,000,000 records. Elapsed time: 00:02:06s. Time for last 1,000,000: 1s. Last read position: chr19:49,490,532
INFO 2026-05-28 20:16:15 MarkDuplicates Tracking 28561 as yet unmatched pairs. 1592 records in RAM.
INFO 2026-05-28 20:16:17 MarkDuplicates Read 67,000,000 records. Elapsed time: 00:02:08s. Time for last 1,000,000: 1s. Last read position: chr20:2,484,216
INFO 2026-05-28 20:16:17 MarkDuplicates Tracking 26958 as yet unmatched pairs. 2869 records in RAM.
INFO 2026-05-28 20:16:19 MarkDuplicates Read 68,000,000 records. Elapsed time: 00:02:09s. Time for last 1,000,000: 1s. Last read position: chr20:45,952,339
INFO 2026-05-28 20:16:19 MarkDuplicates Tracking 25429 as yet unmatched pairs. 1333 records in RAM.
INFO 2026-05-28 20:16:21 MarkDuplicates Read 69,000,000 records. Elapsed time: 00:02:11s. Time for last 1,000,000: 1s. Last read position: chr21:8,214,701
INFO 2026-05-28 20:16:21 MarkDuplicates Tracking 23857 as yet unmatched pairs. 8161 records in RAM.
INFO 2026-05-28 20:16:22 MarkDuplicates Read 70,000,000 records. Elapsed time: 00:02:13s. Time for last 1,000,000: 1s. Last read position: chr21:8,217,026
INFO 2026-05-28 20:16:22 MarkDuplicates Tracking 22299 as yet unmatched pairs. 6572 records in RAM.
INFO 2026-05-28 20:16:23 MarkDuplicates Read 71,000,000 records. Elapsed time: 00:02:14s. Time for last 1,000,000: 1s. Last read position: chr21:8,258,948
INFO 2026-05-28 20:16:23 MarkDuplicates Tracking 21947 as yet unmatched pairs. 6220 records in RAM.
INFO 2026-05-28 20:16:25 MarkDuplicates Read 72,000,000 records. Elapsed time: 00:02:15s. Time for last 1,000,000: 1s. Last read position: chr21:8,397,817
INFO 2026-05-28 20:16:25 MarkDuplicates Tracking 21089 as yet unmatched pairs. 5357 records in RAM.
INFO 2026-05-28 20:16:26 MarkDuplicates Read 73,000,000 records. Elapsed time: 00:02:16s. Time for last 1,000,000: 1s. Last read position: chr21:8,400,357
INFO 2026-05-28 20:16:26 MarkDuplicates Tracking 18879 as yet unmatched pairs. 3119 records in RAM.
INFO 2026-05-28 20:16:27 MarkDuplicates Read 74,000,000 records. Elapsed time: 00:02:18s. Time for last 1,000,000: 1s. Last read position: chr21:8,442,047
INFO 2026-05-28 20:16:27 MarkDuplicates Tracking 18325 as yet unmatched pairs. 2562 records in RAM.
INFO 2026-05-28 20:16:29 MarkDuplicates Read 75,000,000 records. Elapsed time: 00:02:19s. Time for last 1,000,000: 1s. Last read position: chr21:8,444,587
INFO 2026-05-28 20:16:29 MarkDuplicates Tracking 17545 as yet unmatched pairs. 1779 records in RAM.
INFO 2026-05-28 20:16:31 MarkDuplicates Read 76,000,000 records. Elapsed time: 00:02:21s. Time for last 1,000,000: 2s. Last read position: chr21:46,124,658
INFO 2026-05-28 20:16:31 MarkDuplicates Tracking 15993 as yet unmatched pairs. 226 records in RAM.
INFO 2026-05-28 20:16:32 MarkDuplicates Read 77,000,000 records. Elapsed time: 00:02:23s. Time for last 1,000,000: 1s. Last read position: chr22:37,312,105
INFO 2026-05-28 20:16:32 MarkDuplicates Tracking 14194 as yet unmatched pairs. 1804 records in RAM.
INFO 2026-05-28 20:16:34 MarkDuplicates Read 78,000,000 records. Elapsed time: 00:02:25s. Time for last 1,000,000: 1s. Last read position: chrX:2,726,309
INFO 2026-05-28 20:16:34 MarkDuplicates Tracking 12288 as yet unmatched pairs. 2500 records in RAM.
INFO 2026-05-28 20:16:36 MarkDuplicates Read 79,000,000 records. Elapsed time: 00:02:27s. Time for last 1,000,000: 1s. Last read position: chrX:101,391,503
INFO 2026-05-28 20:16:36 MarkDuplicates Tracking 10962 as yet unmatched pairs. 1060 records in RAM.
INFO 2026-05-28 20:16:38 MarkDuplicates Read 80,000,000 records. Elapsed time: 00:02:28s. Time for last 1,000,000: 1s. Last read position: GL000220.1:114,119
INFO 2026-05-28 20:16:38 MarkDuplicates Tracking 9702 as yet unmatched pairs. 2882 records in RAM.
INFO 2026-05-28 20:16:39 MarkDuplicates Read 81,000,000 records. Elapsed time: 00:02:29s. Time for last 1,000,000: 1s. Last read position: GL000220.1:115,558
INFO 2026-05-28 20:16:39 MarkDuplicates Tracking 6977 as yet unmatched pairs. 157 records in RAM.
INFO 2026-05-28 20:16:40 MarkDuplicates Read 82,000,000 records. Elapsed time: 00:02:31s. Time for last 1,000,000: 1s. Last read position: GL000220.1:157,871
INFO 2026-05-28 20:16:40 MarkDuplicates Tracking 6998 as yet unmatched pairs. 178 records in RAM.
INFO 2026-05-28 20:16:41 MarkDuplicates Read 83,000,000 records. Elapsed time: 00:02:32s. Time for last 1,000,000: 1s. Last read position: GL000220.1:159,525
INFO 2026-05-28 20:16:41 MarkDuplicates Tracking 6845 as yet unmatched pairs. 25 records in RAM.
INFO 2026-05-28 20:16:43 MarkDuplicates Read 84,000,000 records. Elapsed time: 00:02:33s. Time for last 1,000,000: 1s. Last read position: KI270733.1:129,665
INFO 2026-05-28 20:16:43 MarkDuplicates Tracking 6780 as yet unmatched pairs. 6779 records in RAM.
INFO 2026-05-28 20:16:44 MarkDuplicates Read 85,000,000 records. Elapsed time: 00:02:35s. Time for last 1,000,000: 1s. Last read position: KI270733.1:132,403
INFO 2026-05-28 20:16:44 MarkDuplicates Tracking 1204 as yet unmatched pairs. 1203 records in RAM.
INFO 2026-05-28 20:16:46 MarkDuplicates Read 86,000,000 records. Elapsed time: 00:02:36s. Time for last 1,000,000: 1s. Last read position: KI270733.1:171,711
INFO 2026-05-28 20:16:46 MarkDuplicates Tracking 335 as yet unmatched pairs. 334 records in RAM.
INFO 2026-05-28 20:16:47 MarkDuplicates Read 87,000,000 records. Elapsed time: 00:02:37s. Time for last 1,000,000: 1s. Last read position: KI270733.1:176,713
INFO 2026-05-28 20:16:47 MarkDuplicates Tracking 101 as yet unmatched pairs. 100 records in RAM.
INFO 2026-05-28 20:16:48 MarkDuplicates Read 88,000,000 records. Elapsed time: 00:02:39s. Time for last 1,000,000: 1s. Last read position: KI270733.1:179,526
INFO 2026-05-28 20:16:48 MarkDuplicates Tracking 1 as yet unmatched pairs. 0 records in RAM.
INFO 2026-05-28 20:16:48 MarkDuplicates Read 88010500 records. 0 pairs never matched.
INFO 2026-05-28 20:16:51 MarkDuplicates After buildSortedReadEndLists freeMemory: 25249714016; totalMemory: 36037459968; maxMemory: 63585648640
INFO 2026-05-28 20:16:51 MarkDuplicates Will retain up to 1987051520 duplicate indices before spilling to disk.
INFO 2026-05-28 20:16:55 MarkDuplicates Traversing read pair information and detecting duplicates.
INFO 2026-05-28 20:17:08 OpticalDuplicateFinder Large duplicate set. size = 1441
INFO 2026-05-28 20:17:08 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:8,685
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder Large duplicate set. size = 1742
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,660
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder Large duplicate set. size = 1212
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-27,727
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder Large duplicate set. size = 1088
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:18,337
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder Large duplicate set. size = 1182
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:9,365
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder Large duplicate set. size = 1276
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:19,720
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder Large duplicate set. size = 1154
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:14,980
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder Large duplicate set. size = 1930
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:10,765
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder Large duplicate set. size = 1279
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-23,026
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder Large duplicate set. size = 1159
INFO 2026-05-28 20:17:12 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-24,749
INFO 2026-05-28 20:17:13 OpticalDuplicateFinder Large duplicate set. size = 1333
INFO 2026-05-28 20:17:13 OpticalDuplicateFinder compared 1,000 ReadEnds to others. Elapsed time: 00:00:00s. Time for last 1,000: 0s. Last read position: 0:-28,705
INFO 2026-05-28 20:17:13 MarkDuplicates Traversing fragment information and detecting duplicates.
INFO 2026-05-28 20:17:20 MarkDuplicates Sorting list of duplicate records.
INFO 2026-05-28 20:17:23 MarkDuplicates After generateDuplicateIndexes freeMemory: 30824784096; totalMemory: 46774878208; maxMemory: 63585648640
INFO 2026-05-28 20:17:23 MarkDuplicates Marking 59021926 records as duplicates.
INFO 2026-05-28 20:17:23 MarkDuplicates Found 1243771 optical duplicate clusters.
INFO 2026-05-28 20:17:23 MarkDuplicates Reads are assumed to be ordered by: coordinate
INFO 2026-05-28 20:17:44 MarkDuplicates Written 10,000,000 records. Elapsed time: 00:00:20s. Time for last 10,000,000: 20s. Last read position: chr2:188,994,548
INFO 2026-05-28 20:18:04 MarkDuplicates Written 20,000,000 records. Elapsed time: 00:00:40s. Time for last 10,000,000: 20s. Last read position: chr6:15,334,513
INFO 2026-05-28 20:18:36 MarkDuplicates Written 30,000,000 records. Elapsed time: 00:01:12s. Time for last 10,000,000: 31s. Last read position: chr9:14,116,232
INFO 2026-05-28 20:19:05 MarkDuplicates Written 40,000,000 records. Elapsed time: 00:01:42s. Time for last 10,000,000: 29s. Last read position: chr12:8,224,718
INFO 2026-05-28 20:19:36 MarkDuplicates Written 50,000,000 records. Elapsed time: 00:02:12s. Time for last 10,000,000: 30s. Last read position: chr16:15,127,728
INFO 2026-05-28 20:20:09 MarkDuplicates Written 60,000,000 records. Elapsed time: 00:02:45s. Time for last 10,000,000: 32s. Last read position: chr17:81,512,113
INFO 2026-05-28 20:20:37 MarkDuplicates Written 70,000,000 records. Elapsed time: 00:03:14s. Time for last 10,000,000: 28s. Last read position: chr21:8,217,026
INFO 2026-05-28 20:21:08 MarkDuplicates Written 80,000,000 records. Elapsed time: 00:03:44s. Time for last 10,000,000: 30s. Last read position: GL000220.1:114,119
INFO 2026-05-28 20:21:33 MarkDuplicates Writing complete. Closing input iterator.
INFO 2026-05-28 20:21:33 MarkDuplicates Duplicate Index cleanup.
INFO 2026-05-28 20:21:33 MarkDuplicates Getting Memory Stats.
INFO 2026-05-28 20:21:33 MarkDuplicates Before output close freeMemory: 202430400; totalMemory: 234881024; maxMemory: 63585648640
INFO 2026-05-28 20:21:33 MarkDuplicates Closed outputs. Getting more Memory Stats.
INFO 2026-05-28 20:21:33 MarkDuplicates After output close freeMemory: 104261656; totalMemory: 134217728; maxMemory: 63585648640
[Thu May 28 20:21:33 GMT 2026] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 7.43 minutes.
Runtime.totalMemory()=134217728
Tool returned:
0
ls: *cram: No such file or directory
ls: *.crai: No such file or directory