Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/659_Em-N1-BDNA-1_B23MHTGLT4_1/659_Em-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/3fda04876b748c9d426c98adba67ac/.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/ca/3fda04876b748c9d426c98adba67ac/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/659_Em-N1-BDNA-1_B23MHTGLT4_1/659_Em-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
==> 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: 659_Em-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Em-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Em-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_Em-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: 78829508 total, 49237 skipped (flags/unmapped)
Fragments: 39597007 total (39146915 tlen-paired, 5185 hash-paired, 433 singletons, 8374 discordant, 436100 orphans, 11395 too large [>5000 bp], 11758810 duplicates)
Reads: 74069771 total, 57290 skipped (flags/unmapped)
Fragments: 37211330 total (36766645 tlen-paired, 5098 hash-paired, 379 singletons, 12592 discordant, 426616 orphans, 8408 too large [>5000 bp], 11271831 duplicates)
Reads: 85731072 total, 56864 skipped (flags/unmapped)
Fragments: 43070970 total (42545645 tlen-paired, 7278 hash-paired, 416 singletons, 12803 discordant, 504828 orphans, 18756 too large [>5000 bp], 13119187 duplicates)
Reads: 87152882 total, 88494 skipped (flags/unmapped)
Fragments: 43993234 total (42542522 tlen-paired, 6422 hash-paired, 450 singletons, 281096 discordant, 1162744 orphans, 120557 too large [>5000 bp], 13372423 duplicates)