Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1047_MI-N1-BDNA-1_B23MHTGLT4_1/1047_MI-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_MI-N1-BDNA-1_B23MHTGLT4_1/1047_MI-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/4a600ca3c8abed195644c58be40135/.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/64/4a600ca3c8abed195644c58be40135/.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_MI-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_MI-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_MI-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_MI-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: 82043964 total, 67665 skipped (flags/unmapped)
Fragments: 41226876 total (40711065 tlen-paired, 3064 hash-paired, 505 singletons, 15100 discordant, 497142 orphans, 10097 too large [>5000 bp], 14707041 duplicates)
Reads: 87287371 total, 62532 skipped (flags/unmapped)
Fragments: 43858406 total (43325389 tlen-paired, 3967 hash-paired, 582 singletons, 10013 discordant, 518455 orphans, 13532 too large [>5000 bp], 15320182 duplicates)
Reads: 95591387 total, 63298 skipped (flags/unmapped)
Fragments: 48039127 total (47417100 tlen-paired, 7453 hash-paired, 471 singletons, 15541 discordant, 598562 orphans, 24434 too large [>5000 bp], 17232353 duplicates)
Reads: 97425098 total, 101942 skipped (flags/unmapped)
Fragments: 49202726 total (47506943 tlen-paired, 2991 hash-paired, 482 singletons, 334052 discordant, 1358258 orphans, 138222 too large [>5000 bp], 17551168 duplicates)