Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/92a907f4b4a621079915de3229f2b9/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_627-N1-BDNA-1_B23MHTGLT4_1/1029_627-N1-BDNA-1_B23MHTGLT4_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/8b/92a907f4b4a621079915de3229f2b9/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_627-N1-BDNA-1_B23MHTGLT4_1/1029_627-N1-BDNA-1_B23MHTGLT4_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_627-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_627-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_627-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_627-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: 80484911 total, 49257 skipped (flags/unmapped)
Fragments: 40400562 total (39997434 tlen-paired, 4084 hash-paired, 421 singletons, 11852 discordant, 386771 orphans, 10861 too large [>5000 bp], 12138128 duplicates)
Reads: 81845224 total, 45320 skipped (flags/unmapped)
Fragments: 41075552 total (40693125 tlen-paired, 2554 hash-paired, 449 singletons, 9849 discordant, 369575 orphans, 9412 too large [>5000 bp], 11986904 duplicates)
Reads: 76498682 total, 54765 skipped (flags/unmapped)
Fragments: 38391910 total (38012818 tlen-paired, 2904 hash-paired, 479 singletons, 14047 discordant, 361662 orphans, 11119 too large [>5000 bp], 11462347 duplicates)
Reads: 89255584 total, 77129 skipped (flags/unmapped)
Fragments: 44950592 total (43814548 tlen-paired, 2586 hash-paired, 462 singletons, 224467 discordant, 908529 orphans, 93131 too large [>5000 bp], 13493348 duplicates)