Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a6/1a6706bbf2a5958c2cb324839488e8/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_2FA-N1-BDNA-1_A23MHW3LT4_1/1136_2FA-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0064_A23MHW3LT4__5d7f62c6--20260313-122016/alignments/recalibrated/1136_2FA-N1-BDNA-1_A23MHW3LT4_1/1136_2FA-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
  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/a6/1a6706bbf2a5958c2cb324839488e8/.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: 1136_2FA-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2FA-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2FA-N1-BDNA-1_A23MHW3LT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1136_2FA-N1-BDNA-1_A23MHW3LT4_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: 72949103 total, 39793 skipped (flags/unmapped)
Fragments: 36658468 total (36223467 tlen-paired, 1964 hash-paired, 425 singletons, 9225 discordant, 423387 orphans, 8093 too large [>5000 bp], 12374498 duplicates)
Reads: 68494219 total, 46359 skipped (flags/unmapped)
Fragments: 34419820 total (33993617 tlen-paired, 2666 hash-paired, 425 singletons, 13021 discordant, 410091 orphans, 9368 too large [>5000 bp], 11917919 duplicates)
Reads: 79622532 total, 44985 skipped (flags/unmapped)
Fragments: 40013177 total (39498181 tlen-paired, 3383 hash-paired, 323 singletons, 14438 discordant, 496852 orphans, 24184 too large [>5000 bp], 13865347 duplicates)
Reads: 81160655 total, 76285 skipped (flags/unmapped)
Fragments: 40979658 total (39604323 tlen-paired, 2632 hash-paired, 427 singletons, 268793 discordant, 1103483 orphans, 114482 too large [>5000 bp], 14175907 duplicates)