Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_1D6-N1-BDNA-1_A23TY7KLT4_1/1241_1D6-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260522_LH00527_0093_A23TY7KLT4__8afaba2b--20260524-103028/alignments/recalibrated/1241_1D6-N1-BDNA-1_A23TY7KLT4_1/1241_1D6-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/bea30bb922d8763c9db069942c77e7/.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/24/bea30bb922d8763c9db069942c77e7/.command.run
==> 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: 1241_1D6-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_1D6-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1241_1D6-N1-BDNA-1_A23TY7KLT4_1.recalibrated.bam.bai
Count mode: frac
[W::hts_idx_load3] The index file is older than the data file: 1241_1D6-N1-BDNA-1_A23TY7KLT4_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: 74882313 total, 43930 skipped (flags/unmapped)
Fragments: 37501760 total (37309852 tlen-paired, 3373 hash-paired, 429 singletons, 6898 discordant, 181208 orphans, 8250 too large [>5000 bp], 12545469 duplicates)
Reads: 70178311 total, 51432 skipped (flags/unmapped)
Fragments: 35143628 total (34954748 tlen-paired, 2604 hash-paired, 288 singletons, 10545 discordant, 175443 orphans, 7677 too large [>5000 bp], 11975804 duplicates)
Reads: 81732901 total, 47796 skipped (flags/unmapped)
Fragments: 40932909 total (40700240 tlen-paired, 5679 hash-paired, 264 singletons, 10349 discordant, 216377 orphans, 17964 too large [>5000 bp], 14041577 duplicates)
Reads: 82109762 total, 78454 skipped (flags/unmapped)
Fragments: 41175119 total (40683858 tlen-paired, 2557 hash-paired, 350 singletons, 91650 discordant, 396704 orphans, 39062 too large [>5000 bp], 14176205 duplicates)