Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/659_d13-N1-BDNA-1_B23MHTGLT4_1/659_d13-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/659_d13-N1-BDNA-1_B23MHTGLT4_1/659_d13-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4e/bbbae6300b44f70cd57f275eceb32f/.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/4e/bbbae6300b44f70cd57f275eceb32f/.command.run
==> 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: 659_d13-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.baiThe index file is older than the data file: 659_d13-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai

[W::hts_idx_load3] The index file is older than the data file: 659_d13-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_d13-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: 66251727 total, 52378 skipped (flags/unmapped)
Fragments: 33241130 total (32930265 tlen-paired, 3659 hash-paired, 380 singletons, 10757 discordant, 296069 orphans, 6769 too large [>5000 bp], 10286008 duplicates)
Reads: 70299409 total, 43177 skipped (flags/unmapped)
Fragments: 35271426 total (34957146 tlen-paired, 3213 hash-paired, 365 singletons, 7243 discordant, 303459 orphans, 8602 too large [>5000 bp], 10712185 duplicates)
Reads: 76970719 total, 47140 skipped (flags/unmapped)
Fragments: 38621089 total (38261087 tlen-paired, 5064 hash-paired, 375 singletons, 11309 discordant, 343254 orphans, 12515 too large [>5000 bp], 12043305 duplicates)
Reads: 77385370 total, 76170 skipped (flags/unmapped)
Fragments: 38964370 total (38004673 tlen-paired, 1933 hash-paired, 397 singletons, 184766 discordant, 772601 orphans, 76729 too large [>5000 bp], 12122539 duplicates)