Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/cc4e003c717518ea62fe16997b1498/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/germline_rescue_targets.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/cc4e003c717518ea62fe16997b1498/.command.run
==> STAGING COMPLETE (7 inputs)

2026-05-28 23:01:13.140584: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 AVX512F AVX512_VNNI FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
I0528 23:01:14.863972 140041175770944 run_deepvariant.py:513] Creating a directory for intermediate results in tmp

***** Intermediate results will be written to tmp in docker. ****


***** Running the command:*****
time seq 0 3 | parallel -q --halt 2 --line-buffer /opt/deepvariant/bin/make_examples --mode calling --ref "Homo_sapiens_assembly38.fasta" --reads "HCC1395_BL.recalibrated.bam" --examples "tmp/make_examples.tfrecord@4.gz" --channels "insert_size" --gvcf "tmp/gvcf.tfrecord@4.gz" --regions "germline_rescue_targets.bed" --task {}

[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0528 23:01:17.208149 139828212098880 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 23:01:17.213194 139828212098880 make_examples_core.py:301] Task 2/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0528 23:01:17.225337 139828212098880 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0528 23:01:17.222421 140010609551168 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 23:01:17.227245 140010609551168 make_examples_core.py:301] Task 0/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0528 23:01:17.239485 140010609551168 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0528 23:01:17.256079 140661833336640 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 23:01:17.260822 140661833336640 make_examples_core.py:301] Task 3/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0528 23:01:17.272914 140661833336640 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0528 23:01:17.246300 140719890601792 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 23:01:17.251062 140719890601792 make_examples_core.py:301] Task 1/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0528 23:01:17.263108 140719890601792 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 23:01:17.623475 139828212098880 make_examples_core.py:301] Task 2/4: Common contigs are ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chrM']
I0528 23:01:17.743359 140010609551168 make_examples_core.py:301] Task 0/4: Common contigs are ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chrM']
I0528 23:01:17.669244 140661833336640 make_examples_core.py:301] Task 3/4: Common contigs are ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chrM']
I0528 23:01:17.652986 140719890601792 make_examples_core.py:301] Task 1/4: Common contigs are ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'chrM']
I0528 23:01:17.910200 139828212098880 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0528 23:01:18.057209 140010609551168 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0528 23:01:17.961642 140661833336640 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0528 23:01:17.944846 140719890601792 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0528 23:01:18.274744 139828212098880 make_examples_core.py:301] Task 2/4: Starting from v0.9.0, --use_ref_for_cram is default to true. If you are using CRAM input, note that we will decode CRAM using the reference you passed in with --ref
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0528 23:01:18.346980 139828212098880 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0528 23:01:18.408447 140010609551168 make_examples_core.py:301] Task 0/4: Starting from v0.9.0, --use_ref_for_cram is default to true. If you are using CRAM input, note that we will decode CRAM using the reference you passed in with --ref
I0528 23:01:18.321794 140661833336640 make_examples_core.py:301] Task 3/4: Starting from v0.9.0, --use_ref_for_cram is default to true. If you are using CRAM input, note that we will decode CRAM using the reference you passed in with --ref
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0528 23:01:18.393403 140661833336640 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 23:01:18.310791 140719890601792 make_examples_core.py:301] Task 1/4: Starting from v0.9.0, --use_ref_for_cram is default to true. If you are using CRAM input, note that we will decode CRAM using the reference you passed in with --ref
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0528 23:01:18.389582 140719890601792 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 23:01:18.416898 139828212098880 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 23:01:18.417658 139828212098880 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0528 23:01:18.418087 139828212098880 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0528 23:01:18.418146 139828212098880 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 1 seconds
I0528 23:01:18.421214 139828212098880 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0528 23:01:18.479148 140010609551168 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0528 23:01:18.551105 140010609551168 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 23:01:18.551893 140010609551168 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0528 23:01:18.552346 140010609551168 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0528 23:01:18.552408 140010609551168 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 1 seconds
I0528 23:01:18.556091 140010609551168 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0528 23:01:18.462812 140661833336640 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 23:01:18.463593 140661833336640 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0528 23:01:18.464014 140661833336640 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0528 23:01:18.464073 140661833336640 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 1 seconds
I0528 23:01:18.466787 140661833336640 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0528 23:01:18.460631 140719890601792 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 23:01:18.461407 140719890601792 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0528 23:01:18.461923 140719890601792 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0528 23:01:18.461986 140719890601792 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 1 seconds
I0528 23:01:18.464710 140719890601792 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0528 23:01:21.014059 140010609551168 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0528 23:01:21.014189 140010609551168 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0528 23:01:21.014379 140010609551168 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0528 23:01:21.014696 140010609551168 make_examples_core.py:301] Task 0/4: Found 3 candidate variants
I0528 23:01:21.014750 140010609551168 make_examples_core.py:301] Task 0/4: Created 5 examples
I0528 23:01:20.978298 140661833336640 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0528 23:01:20.978417 140661833336640 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0528 23:01:20.978597 140661833336640 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0528 23:01:20.978903 140661833336640 make_examples_core.py:301] Task 3/4: Found 3 candidate variants
I0528 23:01:20.978954 140661833336640 make_examples_core.py:301] Task 3/4: Created 5 examples
I0528 23:01:21.215862 140719890601792 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0528 23:01:21.215989 140719890601792 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0528 23:01:21.216205 140719890601792 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0528 23:01:21.216516 140719890601792 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0528 23:01:21.216567 140719890601792 make_examples_core.py:301] Task 1/4: Created 1 examples
I0528 23:01:21.653301 139828212098880 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0528 23:01:21.653442 139828212098880 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0528 23:01:21.653668 139828212098880 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0528 23:01:21.654025 139828212098880 make_examples_core.py:301] Task 2/4: Found 6 candidate variants
I0528 23:01:21.654096 139828212098880 make_examples_core.py:301] Task 2/4: Created 6 examples

real	0m7.163s
user	0m26.434s
sys	0m10.994s

***** Running the command:*****
time /opt/deepvariant/bin/call_variants --outfile "tmp/call_variants_output.tfrecord.gz" --examples "tmp/make_examples.tfrecord@4.gz" --checkpoint "/opt/models/wes"

/usr/local/lib/python3.8/dist-packages/tensorflow_addons/utils/tfa_eol_msg.py:23: UserWarning: 

TensorFlow Addons (TFA) has ended development and introduction of new features.
TFA has entered a minimal maintenance and release mode until a planned end of life in May 2024.
Please modify downstream libraries to take dependencies from other repositories in our TensorFlow community (e.g. Keras, Keras-CV, and Keras-NLP). 

For more information see: https://github.com/tensorflow/addons/issues/2807 

  warnings.warn(
I0528 23:01:24.459266 140195623282496 call_variants.py:563] Total 1 writing processes started.
I0528 23:01:24.460958 140195623282496 dv_utils.py:370] From tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json: Shape of input examples: [100, 221, 7], Channels of input examples: [1, 2, 3, 4, 5, 6, 19].
I0528 23:01:24.461025 140195623282496 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0528 23:01:24.461235 140195623282496 call_variants.py:592] Use saved model: True
I0528 23:01:29.786053 140195623282496 dv_utils.py:370] From /opt/models/wes/example_info.json: Shape of input examples: [100, 221, 7], Channels of input examples: [1, 2, 3, 4, 5, 6, 19].
I0528 23:01:29.786278 140195623282496 dv_utils.py:370] From tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json: Shape of input examples: [100, 221, 7], Channels of input examples: [1, 2, 3, 4, 5, 6, 19].
I0528 23:01:30.543206 140195623282496 call_variants.py:716] Predicted 17 examples in 1 batches [3.629 sec per 100].
I0528 23:01:30.608696 140195623282496 call_variants.py:779] Complete: call_variants.

real	0m9.409s
user	0m10.828s
sys	0m9.061s

***** Running the command:*****
time /opt/deepvariant/bin/postprocess_variants --ref "Homo_sapiens_assembly38.fasta" --infile "tmp/call_variants_output.tfrecord.gz" --outfile "HCC1395_BL.dv_rescue.vcf.gz" --cpus "4" --gvcf_outfile "HCC1395_BL.dv_rescue.g.vcf.gz" --nonvariant_site_tfrecord_path "tmp/gvcf.tfrecord@4.gz"

I0528 23:01:33.704452 140715930240832 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-05-28 23:01:33.709858: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-05-28 23:01:33.710014: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 17
I0528 23:01:33.711241 140715930240832 postprocess_variants.py:1313] CVO sorting took 0.00010346571604410807 minutes
I0528 23:01:33.711436 140715930240832 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0528 23:01:33.711474 140715930240832 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0528 23:01:33.737944 140715930240832 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0528 23:01:33.744392 140715930240832 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 5.360841751098633e-05 minutes
I0528 23:01:33.859811 140715930240832 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0019213438034057617 minutes.

real	0m2.736s
user	0m3.806s
sys	0m8.452s

***** Running the command:*****
time /opt/deepvariant/bin/vcf_stats_report --input_vcf "HCC1395_BL.dv_rescue.vcf.gz" --outfile_base "HCC1395_BL.dv_rescue"

I0528 23:01:36.373043 140110665922368 genomics_reader.py:222] Reading HCC1395_BL.dv_rescue.vcf.gz with NativeVcfReader

real	0m2.629s
user	0m3.537s
sys	0m8.213s