Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/77/2c9dfff66bef12305c44bc5cd47b7a/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1047_X-N1-BDNA-1_B23MHTGLT4_1/1047_X-N1-BDNA-1_B23MHTGLT4_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/77/2c9dfff66bef12305c44bc5cd47b7a/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260311_LH00519_0063_B23MHTGLT4__5d7f62c6--20260313-121014/alignments/recalibrated/1047_X-N1-BDNA-1_B23MHTGLT4_1/1047_X-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam
==> STAGING COMPLETE (5 inputs)

Count mode: frac
Count mode: frac
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1047_X-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_X-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1047_X-N1-BDNA-1_B23MHTGLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1047_X-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: 87242483 total, 64296 skipped (flags/unmapped)
Fragments: 43826912 total (43311620 tlen-paired, 4053 hash-paired, 495 singletons, 14920 discordant, 495824 orphans, 10341 too large [>5000 bp], 14370625 duplicates)
Reads: 93268226 total, 56151 skipped (flags/unmapped)
Fragments: 46854213 total (46321242 tlen-paired, 2994 hash-paired, 551 singletons, 10224 discordant, 519202 orphans, 11701 too large [>5000 bp], 15053945 duplicates)
Reads: 92086546 total, 57197 skipped (flags/unmapped)
Fragments: 46271264 total (45713668 tlen-paired, 2866 hash-paired, 493 singletons, 12661 discordant, 541576 orphans, 14445 too large [>5000 bp], 15273625 duplicates)
Reads: 103151793 total, 97381 skipped (flags/unmapped)
Fragments: 52050573 total (50389520 tlen-paired, 3386 hash-paired, 567 singletons, 334089 discordant, 1323011 orphans, 138422 too large [>5000 bp], 17097988 duplicates)