Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/18d1c24c44ee6ae89585e16e2932df/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1173_FM-N1-BDNA-01_B23MHTGLT4_1/1173_FM-N1-BDNA-01_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/ed/18d1c24c44ee6ae89585e16e2932df/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1173_FM-N1-BDNA-01_B23MHTGLT4_1/1173_FM-N1-BDNA-01_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] [W::hts_idx_load3] The index file is older than the data file: 1173_FM-N1-BDNA-01_B23MHTGLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1173_FM-N1-BDNA-01_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_FM-N1-BDNA-01_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_FM-N1-BDNA-01_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: 78566190 total, 47061 skipped (flags/unmapped)
Fragments: 39422636 total (39065160 tlen-paired, 3142 hash-paired, 458 singletons, 9453 discordant, 344423 orphans, 9369 too large [>5000 bp], 11863430 duplicates)
Reads: 75009945 total, 56417 skipped (flags/unmapped)
Fragments: 37639373 total (37276644 tlen-paired, 2633 hash-paired, 395 singletons, 14420 discordant, 345281 orphans, 10229 too large [>5000 bp], 11542056 duplicates)
Reads: 85762997 total, 50417 skipped (flags/unmapped)
Fragments: 43039156 total (42614845 tlen-paired, 3023 hash-paired, 417 singletons, 14780 discordant, 406091 orphans, 20388 too large [>5000 bp], 13280447 duplicates)
Reads: 87077487 total, 86282 skipped (flags/unmapped)
Fragments: 43836715 total (42767382 tlen-paired, 3669 hash-paired, 479 singletons, 204773 discordant, 860412 orphans, 89333 too large [>5000 bp], 13517363 duplicates)