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/a8/3c797660c7886eca13589723ca505e/.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-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/a8/3c797660c7886eca13589723ca505e/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/8eee459d74eba64dfe5bc8368d5cb4/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e4/8eee459d74eba64dfe5bc8368d5cb4/Sig_18_Blood.recalibrated.bam
==> STAGING COMPLETE (7 inputs)

2026-06-04 17:04:35.458373: 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.
I0604 17:04:37.657792 139938199611200 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 "Sig_18_Blood.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: Sig_18_Blood.recalibrated.bam.bai
I0604 17:04:40.640788 140610433951552 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0604 17:04:40.579891 139852763047744 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:04:40.592208 139852763047744 make_examples_core.py:301] Task 1/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0604 17:04:40.607520 139852763047744 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:04:40.651945 140610433951552 make_examples_core.py:301] Task 3/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0604 17:04:40.667058 140610433951552 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0604 17:04:40.646859 139796432197440 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:04:40.657534 139796432197440 make_examples_core.py:301] Task 2/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0604 17:04:40.672532 139796432197440 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0604 17:04:40.664146 140695548274496 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:04:40.676029 140695548274496 make_examples_core.py:301] Task 0/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0604 17:04:40.691560 140695548274496 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:04:41.186155 139852763047744 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']
I0604 17:04:41.247999 140610433951552 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']
I0604 17:04:41.550400 139852763047744 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:04:41.252797 139796432197440 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']
I0604 17:04:41.270861 140695548274496 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']
I0604 17:04:41.754423 140610433951552 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:04:41.657339 139796432197440 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:04:41.660703 140695548274496 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:04:42.288207 140610433951552 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: Sig_18_Blood.recalibrated.bam.bai
I0604 17:04:42.344660 140610433951552 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:04:42.033861 139852763047744 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: Sig_18_Blood.recalibrated.bam.bai
I0604 17:04:42.081923 139852763047744 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0604 17:04:42.172851 139852763047744 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:04:42.173818 139852763047744 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0604 17:04:42.174336 139852763047744 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0604 17:04:42.174404 139852763047744 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 1 seconds
I0604 17:04:42.177804 139852763047744 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:04:42.152387 139796432197440 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: Sig_18_Blood.recalibrated.bam.bai
I0604 17:04:42.209551 139796432197440 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0604 17:04:42.302739 139796432197440 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:04:42.303777 139796432197440 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0604 17:04:42.304379 139796432197440 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0604 17:04:42.304454 139796432197440 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 1 seconds
I0604 17:04:42.308552 139796432197440 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:04:42.152598 140695548274496 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
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0604 17:04:42.210286 140695548274496 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0604 17:04:42.303188 140695548274496 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:04:42.304256 140695548274496 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0604 17:04:42.304875 140695548274496 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0604 17:04:42.304958 140695548274496 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 1 seconds
I0604 17:04:42.310093 140695548274496 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.01s elapsed]
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0604 17:04:42.451942 140610433951552 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:04:42.453042 140610433951552 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0604 17:04:42.453713 140610433951552 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0604 17:04:42.453789 140610433951552 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 1 seconds
I0604 17:04:42.457916 140610433951552 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:04:44.837391 139852763047744 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0604 17:04:44.837632 139852763047744 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:04:44.838135 139852763047744 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:04:44.838680 139852763047744 make_examples_core.py:301] Task 1/4: Found 2 candidate variants
I0604 17:04:44.838753 139852763047744 make_examples_core.py:301] Task 1/4: Created 2 examples
I0604 17:04:45.653131 140610433951552 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0604 17:04:45.653372 140610433951552 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:04:45.653929 140610433951552 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:04:45.654522 140610433951552 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0604 17:04:45.654598 140610433951552 make_examples_core.py:301] Task 3/4: Created 4 examples
I0604 17:04:45.836627 139796432197440 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0604 17:04:45.836864 139796432197440 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:04:45.837347 139796432197440 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:04:45.837844 139796432197440 make_examples_core.py:301] Task 2/4: Found 4 candidate variants
I0604 17:04:45.837914 139796432197440 make_examples_core.py:301] Task 2/4: Created 4 examples
I0604 17:04:46.084863 140695548274496 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0604 17:04:46.085122 140695548274496 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:04:46.085671 140695548274496 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:04:46.086262 140695548274496 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0604 17:04:46.086335 140695548274496 make_examples_core.py:301] Task 0/4: Created 9 examples

real	0m8.933s
user	0m33.131s
sys	0m23.186s

***** 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(
I0604 17:04:49.686892 139976380888896 call_variants.py:563] Total 1 writing processes started.
I0604 17:04:49.688812 139976380888896 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].
I0604 17:04:49.688908 139976380888896 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0604 17:04:49.689241 139976380888896 call_variants.py:592] Use saved model: True
I0604 17:04:56.229836 139976380888896 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].
I0604 17:04:56.230148 139976380888896 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].
I0604 17:04:57.104488 139976380888896 call_variants.py:716] Predicted 19 examples in 1 batches [3.709 sec per 100].
I0604 17:04:57.186479 139976380888896 call_variants.py:779] Complete: call_variants.

real	0m11.543s
user	0m13.601s
sys	0m13.319s

***** Running the command:*****
time /opt/deepvariant/bin/postprocess_variants --ref "Homo_sapiens_assembly38.fasta" --infile "tmp/call_variants_output.tfrecord.gz" --outfile "germline_control_2.dv_rescue.vcf.gz" --cpus "4" --gvcf_outfile "germline_control_2.dv_rescue.g.vcf.gz" --nonvariant_site_tfrecord_path "tmp/gvcf.tfrecord@4.gz"

I0604 17:05:00.689782 140561917830976 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
2026-06-04 17:05:00.695964: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-04 17:05:00.696139: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 19
I0604 17:05:00.697707 140561917830976 postprocess_variants.py:1313] CVO sorting took 0.00012099742889404297 minutes
I0604 17:05:00.697890 140561917830976 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0604 17:05:00.697950 140561917830976 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0604 17:05:00.723690 140561917830976 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
I0604 17:05:00.730497 140561917830976 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 5.005200703938802e-05 minutes
I0604 17:05:00.867206 140561917830976 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0022760907808939616 minutes.

real	0m3.099s
user	0m4.119s
sys	0m12.576s

***** Running the command:*****
time /opt/deepvariant/bin/vcf_stats_report --input_vcf "germline_control_2.dv_rescue.vcf.gz" --outfile_base "germline_control_2.dv_rescue"

I0604 17:05:03.806587 140146487850816 genomics_reader.py:222] Reading germline_control_2.dv_rescue.vcf.gz with NativeVcfReader

real	0m3.083s
user	0m4.199s
sys	0m12.443s