Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/659_c53-N1-BDNA-1_B23MHTGLT4_1/659_c53-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/32/2a4eff555683072dda19a6a4f949e5/.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/32/2a4eff555683072dda19a6a4f949e5/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/659_c53-N1-BDNA-1_B23MHTGLT4_1/659_c53-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_c53-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_c53-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_c53-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_c53-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: 93700592 total, 55803 skipped (flags/unmapped)
Fragments: 47024265 total (46574277 tlen-paired, 3545 hash-paired, 443 singletons, 10648 discordant, 435352 orphans, 16027 too large [>5000 bp], 15069937 duplicates)
Reads: 88651771 total, 63082 skipped (flags/unmapped)
Fragments: 44483689 total (44064500 tlen-paired, 4109 hash-paired, 506 singletons, 12863 discordant, 401711 orphans, 11764 too large [>5000 bp], 14143157 duplicates)
Reads: 94488717 total, 52753 skipped (flags/unmapped)
Fragments: 47417314 total (46986817 tlen-paired, 2937 hash-paired, 580 singletons, 9036 discordant, 417944 orphans, 9930 too large [>5000 bp], 14799665 duplicates)
Reads: 103889685 total, 91302 skipped (flags/unmapped)
Fragments: 52317545 total (50995457 tlen-paired, 3731 hash-paired, 465 singletons, 261758 discordant, 1056134 orphans, 109946 too large [>5000 bp], 16732373 duplicates)