Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b5/69fbd875261ca4954ad372825066d4/.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/b5/69fbd875261ca4954ad372825066d4/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1029_IB4-N1-BDNA-1_B23MHTGLT4_1/1029_IB4-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/1029_IB4-N1-BDNA-1_B23MHTGLT4_1/1029_IB4-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
==> 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: 1029_IB4-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
The index file is older than the data file: 1029_IB4-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IB4-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1029_IB4-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: 65979509 total, 56457 skipped (flags/unmapped)
Fragments: 33139683 total (32751880 tlen-paired, 3901 hash-paired, 377 singletons, 11764 discordant, 371761 orphans, 7912 too large [>5000 bp], 9791451 duplicates)
Reads: 69909793 total, 51469 skipped (flags/unmapped)
Fragments: 35115595 total (34698070 tlen-paired, 5311 hash-paired, 363 singletons, 10294 discordant, 401557 orphans, 14527 too large [>5000 bp], 10420277 duplicates)
Reads: 77592495 total, 80680 skipped (flags/unmapped)
Fragments: 39143714 total (37920045 tlen-paired, 2268 hash-paired, 459 singletons, 243326 discordant, 977616 orphans, 101231 too large [>5000 bp], 11579173 duplicates)
Reads: 71517798 total, 46144 skipped (flags/unmapped)
Fragments: 35921442 total (35520106 tlen-paired, 2492 hash-paired, 464 singletons, 8738 discordant, 389642 orphans, 9438 too large [>5000 bp], 10341766 duplicates)