Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_7JJ-N1-BDNA-1_B23MHTGLT4_1/1136_7JJ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/b8afff7111a6d0339b2feb282f026c/.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/a5/b8afff7111a6d0339b2feb282f026c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1136_7JJ-N1-BDNA-1_B23MHTGLT4_1/1136_7JJ-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: 1136_7JJ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7JJ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7JJ-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_7JJ-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: 101391030 total, 77967 skipped (flags/unmapped)
Fragments: 50855164 total (50407478 tlen-paired, 4125 hash-paired, 654 singletons, 17162 discordant, 425745 orphans, 14567 too large [>5000 bp], 16441571 duplicates)
Reads: 107309243 total, 59679 skipped (flags/unmapped)
Fragments: 53829906 total (53380443 tlen-paired, 5073 hash-paired, 777 singletons, 11546 discordant, 432067 orphans, 11298 too large [>5000 bp], 17150248 duplicates)
Reads: 106623875 total, 67615 skipped (flags/unmapped)
Fragments: 53486192 total (53016227 tlen-paired, 5598 hash-paired, 640 singletons, 14749 discordant, 448978 orphans, 16747 too large [>5000 bp], 17497414 duplicates)
Reads: 117845514 total, 113402 skipped (flags/unmapped)
Fragments: 59284962 total (57962274 tlen-paired, 3792 hash-paired, 665 singletons, 259864 discordant, 1058367 orphans, 110610 too large [>5000 bp], 19400504 duplicates)