Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_500-N1-BDNA-1_B23MHTGLT4_1/1029_500-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/cb01d3941af82e43c33bc7240d656a/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_500-N1-BDNA-1_B23MHTGLT4_1/1029_500-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  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/b3/cb01d3941af82e43c33bc7240d656a/.command.run
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_500-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] [W::hts_idx_load3] The index file is older than the data file: 1029_500-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_500-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1029_500-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Deduplicated 94 probes with identical coordinates
Loaded 472416 probes across 3366 contigs
Reads: 72554684 total, 49115 skipped (flags/unmapped)
Fragments: 36415429 total (36058748 tlen-paired, 2690 hash-paired, 429 singletons, 12656 discordant, 340906 orphans, 8023 too large [>5000 bp], 11431885 duplicates)
Reads: 77695235 total, 43105 skipped (flags/unmapped)
Fragments: 38990780 total (38628585 tlen-paired, 3483 hash-paired, 460 singletons, 8742 discordant, 349510 orphans, 10270 too large [>5000 bp], 11932660 duplicates)
Reads: 76416813 total, 44719 skipped (flags/unmapped)
Fragments: 38357385 total (37960765 tlen-paired, 3220 hash-paired, 355 singletons, 11180 discordant, 381865 orphans, 19772 too large [>5000 bp], 12068719 duplicates)
Reads: 84594785 total, 81484 skipped (flags/unmapped)
Fragments: 42595558 total (41521266 tlen-paired, 3687 hash-paired, 445 singletons, 211494 discordant, 858666 orphans, 90648 too large [>5000 bp], 13382125 duplicates)