Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d2/f5fc9831074525c47252211cf90782/1136_13-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/03cd4d0ba7c7c7d7d1de76792568b3/1029_P0W-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/f40e871691e048abca84407569b225/1029_V13-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/9c47633e79643d71f1f4099425550d/1029_UCZ-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/ea0ccc06e365c655b81c37cf449629/1029_Q3K-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/7cd93d783275e99b835f5767519ee3/1029_BBPA-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/f806606c613b895b0c0c99d05eb348/1029_DQI-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/10/81b028dc5c42d9c7773b17dc1ea201/1029_I2Q-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/d4f8773f47cbe05340be197d89eed0/1029_DB2-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/a2fa932f38e90dcb16e2227e2686fd/1029_G7F-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9e/381f7d655a3940e3bb6a0a5d4988e8/1029_JJU-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/518b75757de1eb3ff049a1a7950e8f/1136_1UN-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/7ac848329293ae820b871c8967aa2f/1029_ROB-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/01/ea31fb5a47b6c192112366d724879c/1029_BQ3K-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/f7b6bf004ce7f9968332156b80ddb9/1029_KET-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/57e37a1117968c48ca721ee3d4b8a2/1029_XPW-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/ce00bfe8b097d731651cc9686967d3/1029_BNM7-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/49/e7cfc588303f02275b97ce9dc9141b/1029_MH0-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/51/9fde2a45584705d3704e704dbaa320/1136_0YQ-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/7cd3a9a707084062114d991d954600/1029_M9U-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/25/475a33366cef95fe78fbbe218381d3/1029_W7S-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/41f978d5afb4712fdc246fc3c17b2a/1029_GNJ-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/284ec86042eb3ec86d41d17cc9cf80/1029_GG5-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a7/2de6b65577deab4dfca41b8b7c5061/1136_10H-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/tmp/2e/bd6a7f4d59ad5db147a949a48c7819/manifest.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/537923eaf0de29863ee342d34d37ef/1029_GP0-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/ac2aa75015ab7720c56938e85f972f/1029_BOCP-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/ae6836a42179c4dd4466b498e70f6c/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/64/ac9c352d5a92045a68fc20ae999eb0/1029_26C-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/be11b0ba28fd5a6f291d302ba23cfa/1029_BCZQ-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/b86217768177629dd1c12b902dff8c/1029_BKJD-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/53312acc4922dd66cb40f66fd83a30/1029_BDK5-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/47/e95e27f61f70db17d2034b1fe02f34/1029_UKQ-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e3/169778de3fd9e48099f14a505fc80f/1029_BL7I-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/39/7222b52bc3d560634cb688f7de4d3e/1029_BC9J-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/2aa774b27aea0bc8b5eb199a121f83/1029_B1C-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/2259d37d412b668fc2991f14b3d356/1029_BLVT-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/bafc325a2266f3c6c3d4f16e252121/1029_BCTD-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8b/8109882332c401fb38737238aa7e78/1029_1CZ-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/1fcce44ccc02384221319b38e13b89/1029_GWX-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/9b3f6f3662e734f634f908ccf7fd38/1029_344-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/a0d07a0e0dc58451c0286fcf900ef0/1029_RCF-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/19140bd76fe07381b55fb97638569d/1029_LNB-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/25b9542a0a278f2ce01a85f6476e93/1029_BNMN-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/36a48c8d92bbe02426960b653f6613/1029_4X0-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dd/e27435c62f5e4aaf34d88b6fe3641c/1029_D19-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/8bee87b1d58732bc52988ab537503e/1029_BI3C-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/ae0211093deca691b931986b5066dc/1029_3HC-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1e/68afd0b4769fec5badef89ad73c26d/1029_1UX-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/85/3371439177e95d07af23dcb6ff3e8f/1029_BPC3-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c7/ae6836a42179c4dd4466b498e70f6c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/02/88b8ca9cfedb427ad446d87e81f872/1136_024-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/63/005df48dd69a09aa1b549cb4238ce0/1136_03N-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/8b05f8974d8b82858d9049125839e9/1029_W1O-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/0040624db6f29407871c08f3c81322/1136_0B-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/02212ba520d852e1a26212e4aa80a6/1029_C3S-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/91/3728898bb6ef40d3f05004ca6371f9/1029_BMDN-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/ab8d6f412040d68f732ab0cc744e19/1029_KR2-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/448b790c0559f18398fdfb8b6673c3/1029_BTW1-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ac/9df8d809765981482eead22ea1e030/1029_NHT-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/7ffc4d68627ae0748f225ca46094a5/1029_BQ0K-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/075cc3c70d45096d6580ba8e36fc0c/1029_7AL-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/0cf40e6622832d91d2278cb380eb8b/1029_BGSQ-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/5165462f80359084222886c3262e0d/1029_YHI-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/457344ca97f2dac3cb5352f141ebc0/1029_WTT-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/cdef5783bf158d0bdb719984087718/1029_BGPR-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/38/9905dc0f15957bf1c57d029211704e/1029_OHN-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/4940c6a265e8523fd4e20b4bec2b4b/1029_BF1C-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/b253d02b43e857f57f9370af709526/1029_22Q-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8a/b1538fde8e429088613e2e402e5b8d/1029_BNY-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/8a182ad4382462673d22239307645d/1136_19H-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/60bdad6afa6e68e168a3f11584978a/1029_7OE-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/668d1782271fb80c344c1b33affa44/1029_3PB-N1-BDNA-1_B23H2GYLT3_1_probes.tsv.gz
==> STAGING COMPLETE (73 inputs)

Blood manifest: 70 samples
Loaded 33,067,020 rows from 70 blood samples in 40.2s
GC reference: 472,386 probes
  Sex chrom homology mask: 1494 probes
  Pass 1: 4-feat blood GAM (16 workers)...
    20/70 blood samples, 24s, R²=0.5114
    40/70 blood samples, 39s, R²=0.5046
    60/70 blood samples, 53s, R²=0.5147
    70/70 blood samples, 59s, R²=0.5395
    Sex: 41 female, 29 male, 0 unknown
/usr/local/bin/build_norm_reference.py:247: RuntimeWarning: All-NaN slice encountered
  probe_coverage_median = np.nanmedian(blood_matrix, axis=1)
/usr/local/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1593: RuntimeWarning: All-NaN slice encountered
  return fnb._ureduce(a,
    Probe coverage: 472,142/472,386 valid probes
  Preliminary 5-feat GAM on blood (16 workers)...
    20/70 blood prelim 5-feat, 52s, R²=0.9278
    40/70 blood prelim 5-feat, 85s, R²=0.9400
    60/70 blood prelim 5-feat, 117s, R²=0.9372
    70/70 blood prelim 5-feat, 124s, R²=0.9337
/usr/local/bin/build_norm_reference.py:335: RuntimeWarning: All-NaN slice encountered
  prelim_median = np.nanmedian(prelim_matrix, axis=1)
/usr/local/lib/python3.12/site-packages/numpy/lib/_nanfunctions_impl.py:1593: RuntimeWarning: All-NaN slice encountered
  return fnb._ureduce(a,
    Probe mask: 11,774 masked (2.5%) — 6,807 low cov, 5,885 high var, 2,569 extreme
Wrote batch_reference.parquet (472,386 probes) to ./batch_reference.parquet
Wrote sex_calls.csv (70 samples) to ./sex_calls.csv
Wrote feature_stats.csv (70 samples) to ./feature_stats.csv
Build reference complete in 437.0s total