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/9e/b96812200c6f14ce427242af600b31/.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/9e/b96812200c6f14ce427242af600b31/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/39fc4609d5b3bb227efea5d5dd4332/Sig_18_Blood.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/39fc4609d5b3bb227efea5d5dd4332/Sig_18_Blood.recalibrated.bam
==> STAGING COMPLETE (7 inputs)
2026-06-08 17:37:08.217110: 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 AVX512_BF16 AVX_VNNI AMX_TILE AMX_INT8 AMX_BF16 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
I0608 17:37:09.528283 140260202465088 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
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0608 17:37:11.536285 139910804502336 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 17:37:11.548669 139910804502336 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
I0608 17:37:11.558112 139910804502336 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
I0608 17:37:11.433411 139885117314880 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 17:37:11.444102 139885117314880 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
I0608 17:37:11.452974 139885117314880 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
I0608 17:37:11.478600 140465842464576 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 17:37:11.490652 140465842464576 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
I0608 17:37:11.499899 140465842464576 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 17:37:11.425964 140126807906112 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 17:37:11.439090 140126807906112 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
I0608 17:37:11.448430 140126807906112 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 17:37:11.721232 139885117314880 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']
I0608 17:37:11.766006 140465842464576 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']
I0608 17:37:11.711660 140126807906112 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']
I0608 17:37:11.839024 139910804502336 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']
I0608 17:37:11.931704 139885117314880 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 17:37:11.919671 140126807906112 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 17:37:12.027144 139910804502336 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 17:37:12.181145 139885117314880 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
I0608 17:37:12.223903 139885117314880 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 17:37:12.025057 140465842464576 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 17:37:12.169461 140126807906112 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
I0608 17:37:12.209776 140126807906112 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 17:37:12.258107 139910804502336 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
I0608 17:37:12.296298 139910804502336 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
I0608 17:37:12.340307 139910804502336 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 17:37:12.340891 139910804502336 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0608 17:37:12.341331 139910804502336 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0608 17:37:12.341388 139910804502336 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0608 17:37:12.343472 139910804502336 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0608 17:37:12.267120 139885117314880 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 17:37:12.267763 139885117314880 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0608 17:37:12.268195 139885117314880 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0608 17:37:12.268257 139885117314880 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0608 17:37:12.271054 139885117314880 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 17:37:12.292463 140465842464576 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
I0608 17:37:12.339875 140465842464576 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
I0608 17:37:12.385820 140465842464576 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 17:37:12.386554 140465842464576 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0608 17:37:12.386965 140465842464576 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0608 17:37:12.387036 140465842464576 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0608 17:37:12.389780 140465842464576 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: Sig_18_Blood.recalibrated.bam.bai
I0608 17:37:12.253384 140126807906112 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 17:37:12.254024 140126807906112 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0608 17:37:12.254431 140126807906112 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0608 17:37:12.254485 140126807906112 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0608 17:37:12.256668 140126807906112 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 17:37:14.065084 140126807906112 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0608 17:37:14.065283 140126807906112 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 17:37:14.065730 140126807906112 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 17:37:14.066218 140126807906112 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0608 17:37:14.066257 140126807906112 make_examples_core.py:301] Task 3/4: Created 4 examples
I0608 17:37:14.601721 140465842464576 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0608 17:37:14.602100 140465842464576 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 17:37:14.603073 140465842464576 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 17:37:14.603802 140465842464576 make_examples_core.py:301] Task 2/4: Found 4 candidate variants
I0608 17:37:14.603853 140465842464576 make_examples_core.py:301] Task 2/4: Created 4 examples
I0608 17:37:14.700162 139910804502336 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0608 17:37:14.700335 139910804502336 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 17:37:14.700736 139910804502336 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 17:37:14.701140 139910804502336 make_examples_core.py:301] Task 1/4: Found 2 candidate variants
I0608 17:37:14.701170 139910804502336 make_examples_core.py:301] Task 1/4: Created 2 examples
I0608 17:37:14.797141 139885117314880 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0608 17:37:14.797383 139885117314880 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 17:37:14.797846 139885117314880 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 17:37:14.798285 139885117314880 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0608 17:37:14.798317 139885117314880 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m5.594s
user 0m31.110s
sys 0m40.158s
***** 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(
I0608 17:37:17.069764 140607847376704 call_variants.py:563] Total 1 writing processes started.
I0608 17:37:17.071356 140607847376704 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].
I0608 17:37:17.071431 140607847376704 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0608 17:37:17.071700 140607847376704 call_variants.py:592] Use saved model: True
I0608 17:37:21.413486 140607847376704 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].
I0608 17:37:21.413701 140607847376704 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].
I0608 17:37:22.222700 140607847376704 call_variants.py:716] Predicted 19 examples in 1 batches [3.618 sec per 100].
I0608 17:37:22.348740 140607847376704 call_variants.py:779] Complete: call_variants.
real 0m8.096s
user 0m11.615s
sys 0m18.521s
***** 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"
I0608 17:37:25.012303 139711068624704 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
2026-06-08 17:37:25.016290: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-08 17:37:25.016451: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 19
I0608 17:37:25.017486 139711068624704 postprocess_variants.py:1313] CVO sorting took 7.783174514770508e-05 minutes
I0608 17:37:25.017687 139711068624704 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0608 17:37:25.017721 139711068624704 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0608 17:37:25.038425 139711068624704 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
I0608 17:37:25.044092 139711068624704 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 5.094210306803385e-05 minutes
I0608 17:37:25.138854 139711068624704 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0015769561131795248 minutes.
real 0m2.213s
user 0m4.771s
sys 0m10.023s
***** 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"
I0608 17:37:27.143346 140227779934016 genomics_reader.py:222] Reading germline_control_2.dv_rescue.vcf.gz with NativeVcfReader
real 0m2.184s
user 0m5.132s
sys 0m9.607s