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/b4/a5fc5a0c43c0a98c1f39d2012df361/.command.sh
Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/Sig_18_Blood/Sig_18_Blood.recal.bam
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-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/Sig_18_Blood/Sig_18_Blood.recal.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/a5fc5a0c43c0a98c1f39d2012df361/.command.run
==> STAGING COMPLETE (7 inputs)
2026-06-04 17:17:41.057689: 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.
I0604 17:17:42.396636 140110814766912 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.recal.bam" --examples "tmp/make_examples.tfrecord@4.gz" --channels "insert_size" --gvcf "tmp/gvcf.tfrecord@4.gz" --regions "germline_rescue_targets.bed" --task {}
I0604 17:17:44.272931 140489860388672 genomics_reader.py:222] Reading Sig_18_Blood.recal.bam with NativeSamReader
I0604 17:17:44.248569 140054844204864 genomics_reader.py:222] Reading Sig_18_Blood.recal.bam with NativeSamReader
I0604 17:17:44.260731 140054844204864 make_examples_core.py:301] Task 1/4: Preparing inputs
I0604 17:17:44.269963 140054844204864 genomics_reader.py:222] Reading Sig_18_Blood.recal.bam with NativeSamReader
I0604 17:17:44.275250 139923761948480 genomics_reader.py:222] Reading Sig_18_Blood.recal.bam with NativeSamReader
I0604 17:17:44.271372 140107733641024 genomics_reader.py:222] Reading Sig_18_Blood.recal.bam with NativeSamReader
I0604 17:17:44.283966 140489860388672 make_examples_core.py:301] Task 3/4: Preparing inputs
I0604 17:17:44.292938 140489860388672 genomics_reader.py:222] Reading Sig_18_Blood.recal.bam with NativeSamReader
I0604 17:17:44.285742 139923761948480 make_examples_core.py:301] Task 0/4: Preparing inputs
I0604 17:17:44.294852 139923761948480 genomics_reader.py:222] Reading Sig_18_Blood.recal.bam with NativeSamReader
I0604 17:17:44.282365 140107733641024 make_examples_core.py:301] Task 2/4: Preparing inputs
I0604 17:17:44.291429 140107733641024 genomics_reader.py:222] Reading Sig_18_Blood.recal.bam with NativeSamReader
I0604 17:17:44.572489 140489860388672 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 17:17:44.549151 140054844204864 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 17:17:44.577909 139923761948480 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 17:17:44.573912 140107733641024 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 17:17:44.805866 140489860388672 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:17:44.734531 140054844204864 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:17:44.789549 139923761948480 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:17:44.781990 140107733641024 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:17:45.046515 140489860388672 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
I0604 17:17:44.981539 140054844204864 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
I0604 17:17:45.046353 140054844204864 genomics_reader.py:222] Reading Sig_18_Blood.recal.bam with NativeSamReader
I0604 17:17:45.089156 140054844204864 genomics_reader.py:222] Reading Sig_18_Blood.recal.bam with NativeSamReader
I0604 17:17:45.029285 139923761948480 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
I0604 17:17:45.027635 140107733641024 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
I0604 17:17:45.110875 140489860388672 genomics_reader.py:222] Reading Sig_18_Blood.recal.bam with NativeSamReader
I0604 17:17:45.154688 140489860388672 genomics_reader.py:222] Reading Sig_18_Blood.recal.bam with NativeSamReader
I0604 17:17:45.155207 140489860388672 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0604 17:17:45.155635 140489860388672 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0604 17:17:45.155685 140489860388672 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0604 17:17:45.158303 140489860388672 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:17:45.089690 140054844204864 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0604 17:17:45.090114 140054844204864 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0604 17:17:45.090170 140054844204864 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0604 17:17:45.092807 140054844204864 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:17:45.097060 139923761948480 genomics_reader.py:222] Reading Sig_18_Blood.recal.bam with NativeSamReader
I0604 17:17:45.139966 139923761948480 genomics_reader.py:222] Reading Sig_18_Blood.recal.bam with NativeSamReader
I0604 17:17:45.140497 139923761948480 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0604 17:17:45.140899 139923761948480 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0604 17:17:45.140952 139923761948480 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0604 17:17:45.144295 139923761948480 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:17:45.097066 140107733641024 genomics_reader.py:222] Reading Sig_18_Blood.recal.bam with NativeSamReader
I0604 17:17:45.139986 140107733641024 genomics_reader.py:222] Reading Sig_18_Blood.recal.bam with NativeSamReader
I0604 17:17:45.140532 140107733641024 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0604 17:17:45.140983 140107733641024 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0604 17:17:45.141039 140107733641024 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0604 17:17:45.144125 140107733641024 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:17:46.929343 140489860388672 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0604 17:17:46.929594 140489860388672 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:17:46.930452 140489860388672 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:17:46.930918 140489860388672 make_examples_core.py:301] Task 3/4: Found 1 candidate variants
I0604 17:17:46.930948 140489860388672 make_examples_core.py:301] Task 3/4: Created 1 examples
I0604 17:17:46.991194 140054844204864 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0604 17:17:46.991408 140054844204864 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:17:46.991842 140054844204864 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:17:46.992264 140054844204864 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0604 17:17:46.992295 140054844204864 make_examples_core.py:301] Task 1/4: Created 1 examples
I0604 17:17:47.122074 140107733641024 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0604 17:17:47.122444 140107733641024 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:17:47.123060 140107733641024 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:17:47.123832 140107733641024 make_examples_core.py:301] Task 2/4: Found 3 candidate variants
I0604 17:17:47.123886 140107733641024 make_examples_core.py:301] Task 2/4: Created 5 examples
I0604 17:17:48.342877 139923761948480 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0604 17:17:48.343259 139923761948480 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:17:48.343858 139923761948480 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:17:48.344583 139923761948480 make_examples_core.py:301] Task 0/4: Found 3 candidate variants
I0604 17:17:48.344639 139923761948480 make_examples_core.py:301] Task 0/4: Created 8 examples
real 0m6.236s
user 0m24.324s
sys 0m37.051s
***** 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 17:17:50.493285 139738529072960 call_variants.py:563] Total 1 writing processes started.
I0604 17:17:50.494795 139738529072960 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 17:17:50.494850 139738529072960 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0604 17:17:50.495069 139738529072960 call_variants.py:592] Use saved model: True
I0604 17:17:54.371213 139738529072960 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 17:17:54.371498 139738529072960 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 17:17:55.072935 139738529072960 call_variants.py:716] Predicted 15 examples in 1 batches [3.824 sec per 100].
I0604 17:17:55.157632 139738529072960 call_variants.py:779] Complete: call_variants.
real 0m7.377s
user 0m11.235s
sys 0m12.759s
***** Running the command:*****
time /opt/deepvariant/bin/postprocess_variants --ref "Homo_sapiens_assembly38.fasta" --infile "tmp/call_variants_output.tfrecord.gz" --outfile "Sig_18_Blood.dv_rescue.vcf.gz" --cpus "4" --gvcf_outfile "Sig_18_Blood.dv_rescue.g.vcf.gz" --nonvariant_site_tfrecord_path "tmp/gvcf.tfrecord@4.gz"
I0604 17:17:57.725184 140132267538240 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
2026-06-04 17:17:57.728948: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-04 17:17:57.729074: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 15
I0604 17:17:57.730079 140132267538240 postprocess_variants.py:1313] CVO sorting took 7.42793083190918e-05 minutes
I0604 17:17:57.730225 140132267538240 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0604 17:17:57.730254 140132267538240 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0604 17:17:57.754718 140132267538240 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
I0604 17:17:57.761870 140132267538240 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 5.097786585489909e-05 minutes
I0604 17:17:57.865419 140132267538240 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.001723647117614746 minutes.
real 0m2.090s
user 0m4.653s
sys 0m11.599s
***** Running the command:*****
time /opt/deepvariant/bin/vcf_stats_report --input_vcf "Sig_18_Blood.dv_rescue.vcf.gz" --outfile_base "Sig_18_Blood.dv_rescue"
I0604 17:17:59.851493 140687175997248 genomics_reader.py:222] Reading Sig_18_Blood.dv_rescue.vcf.gz with NativeVcfReader
real 0m2.008s
user 0m4.915s
sys 0m11.222s