Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_H34-N1-BDNA-1_B23MHTGLT4_1/1029_H34-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_H34-N1-BDNA-1_B23MHTGLT4_1/1029_H34-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/07078764bf8f08290625c429f4d62c/.command.sh
  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/54/07078764bf8f08290625c429f4d62c/.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_H34-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_H34-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_H34-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_H34-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: 74316561 total, 54865 skipped (flags/unmapped)
Fragments: 37291377 total (36936859 tlen-paired, 2724 hash-paired, 405 singletons, 12980 discordant, 338409 orphans, 8878 too large [>5000 bp], 11586687 duplicates)
Reads: 78712561 total, 49124 skipped (flags/unmapped)
Fragments: 39494679 total (39136562 tlen-paired, 3067 hash-paired, 508 singletons, 8347 discordant, 346195 orphans, 10391 too large [>5000 bp], 12028296 duplicates)
Reads: 86212268 total, 51658 skipped (flags/unmapped)
Fragments: 43264669 total (42841056 tlen-paired, 4323 hash-paired, 418 singletons, 12890 discordant, 405982 orphans, 18836 too large [>5000 bp], 13508772 duplicates)
Reads: 86975991 total, 90175 skipped (flags/unmapped)
Fragments: 43791461 total (42697498 tlen-paired, 3295 hash-paired, 478 singletons, 212580 discordant, 877610 orphans, 90491 too large [>5000 bp], 13640515 duplicates)