Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1047_MK-N1-BDNA-1_B23MHTGLT4_1/1047_MK-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/1047_MK-N1-BDNA-1_B23MHTGLT4_1/1047_MK-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/04d50afd3f4f70707f5bab077d5611/.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/47/04d50afd3f4f70707f5bab077d5611/.command.run
==> 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: 1047_MK-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_MK-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_MK-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_MK-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: 70837827 total, 51369 skipped (flags/unmapped)
Fragments: 35591334 total (35160980 tlen-paired, 2641 hash-paired, 506 singletons, 11103 discordant, 416104 orphans, 10200 too large [>5000 bp], 11262850 duplicates)
Reads: 75439181 total, 44877 skipped (flags/unmapped)
Fragments: 37904865 total (37463192 tlen-paired, 2229 hash-paired, 560 singletons, 7666 discordant, 431218 orphans, 8176 too large [>5000 bp], 11710554 duplicates)
Reads: 75057286 total, 48381 skipped (flags/unmapped)
Fragments: 37711489 total (37253671 tlen-paired, 2808 hash-paired, 395 singletons, 9409 discordant, 445206 orphans, 15764 too large [>5000 bp], 11992686 duplicates)
Reads: 83502047 total, 78707 skipped (flags/unmapped)
Fragments: 42153902 total (40741667 tlen-paired, 2632 hash-paired, 505 singletons, 285297 discordant, 1123801 orphans, 119921 too large [>5000 bp], 13344301 duplicates)