Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/1592433417e4cadf38a808df83ac30/.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/ca/1592433417e4cadf38a808df83ac30/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_FE-N1-BDNA-1_B23L5TMLT4_1/1047_FE-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260227_LH00519_0059_B23L5TMLT4__444aee1e--20260301-135529/alignments/recalibrated/1047_FE-N1-BDNA-1_B23L5TMLT4_1/1047_FE-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1047_FE-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1047_FE-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_FE-N1-BDNA-1_B23L5TMLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_FE-N1-BDNA-1_B23L5TMLT4_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: 81527287 total, 63631 skipped (flags/unmapped)
Fragments: 40928008 total (40494965 tlen-paired, 3642 hash-paired, 544 singletons, 14315 discordant, 414542 orphans, 11363 too large [>5000 bp], 14766170 duplicates)
Reads: 86852841 total, 54828 skipped (flags/unmapped)
Fragments: 43603610 total (43151680 tlen-paired, 4061 hash-paired, 560 singletons, 10354 discordant, 436955 orphans, 14154 too large [>5000 bp], 15389195 duplicates)
Reads: 86061327 total, 61414 skipped (flags/unmapped)
Fragments: 43210317 total (42733765 tlen-paired, 6831 hash-paired, 422 singletons, 12520 discordant, 456779 orphans, 18240 too large [>5000 bp], 15667061 duplicates)
Reads: 95648346 total, 100315 skipped (flags/unmapped)
Fragments: 48200084 total (46848141 tlen-paired, 3675 hash-paired, 525 singletons, 269509 discordant, 1078234 orphans, 113311 too large [>5000 bp], 17365881 duplicates)