Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/a4da00df2e283a1b840c7baaef6ee9/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_H0D-N1-BDNA-1_A23MHW3LT4_1/1029_H0D-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/a4da00df2e283a1b840c7baaef6ee9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1029_H0D-N1-BDNA-1_A23MHW3LT4_1/1029_H0D-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_H0D-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_H0D-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_H0D-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_H0D-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 83409294 total, 63365 skipped (flags/unmapped)
Fragments: 41891792 total (41408030 tlen-paired, 3457 hash-paired, 471 singletons, 19056 discordant, 460778 orphans, 11797 too large [>5000 bp], 13718511 duplicates)
Reads: 88537565 total, 54870 skipped (flags/unmapped)
Fragments: 44461825 total (43973183 tlen-paired, 4191 hash-paired, 534 singletons, 13006 discordant, 470911 orphans, 15245 too large [>5000 bp], 14351455 duplicates)
Reads: 96593973 total, 60099 skipped (flags/unmapped)
Fragments: 48514968 total (47941819 tlen-paired, 6292 hash-paired, 434 singletons, 19819 discordant, 546604 orphans, 25488 too large [>5000 bp], 15984486 duplicates)
Reads: 98224671 total, 98925 skipped (flags/unmapped)
Fragments: 49530824 total (48078596 tlen-paired, 3582 hash-paired, 471 singletons, 279704 discordant, 1168471 orphans, 116520 too large [>5000 bp], 16268878 duplicates)