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/2d/1260f1508d8230f69443df96693585/.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/2d/1260f1508d8230f69443df96693585/.command.run
==> STAGING COMPLETE (7 inputs)
2026-06-04 23:57:42.170925: 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 23:57:43.434183 139766949898048 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 {}
I0604 23:57:45.271091 139648147167040 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 23:57:45.278454 139648147167040 make_examples_core.py:301] Task 3/4: Preparing inputs
I0604 23:57:45.287349 139648147167040 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 23:57:45.289279 140051437832000 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 23:57:45.296010 140051437832000 make_examples_core.py:301] Task 2/4: Preparing inputs
I0604 23:57:45.304853 140051437832000 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 23:57:45.368160 139751548888896 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 23:57:45.374748 139751548888896 make_examples_core.py:301] Task 0/4: Preparing inputs
I0604 23:57:45.383515 139751548888896 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 23:57:45.350585 139798385985344 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 23:57:45.357220 139798385985344 make_examples_core.py:301] Task 1/4: Preparing inputs
I0604 23:57:45.365840 139798385985344 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 23:57:45.555685 139648147167040 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 23:57:45.572761 140051437832000 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 23:57:45.651115 139751548888896 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 23:57:45.634162 139798385985344 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 23:57:45.723951 139648147167040 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 23:57:45.769877 140051437832000 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 23:57:45.881048 139751548888896 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 23:57:45.849357 139798385985344 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 23:57:45.969579 139648147167040 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 23:57:46.028376 139648147167040 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 23:57:46.071921 139648147167040 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 23:57:46.072613 139648147167040 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0604 23:57:46.073075 139648147167040 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0604 23:57:46.073131 139648147167040 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0604 23:57:46.075269 139648147167040 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 23:57:46.042692 140051437832000 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 23:57:46.107729 140051437832000 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 23:57:46.111194 139798385985344 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 23:57:46.151505 140051437832000 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 23:57:46.152244 140051437832000 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0604 23:57:46.152744 140051437832000 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0604 23:57:46.152812 140051437832000 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0604 23:57:46.155263 140051437832000 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 23:57:46.130329 139751548888896 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 23:57:46.190711 139751548888896 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 23:57:46.234031 139751548888896 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 23:57:46.234701 139751548888896 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0604 23:57:46.235119 139751548888896 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0604 23:57:46.235181 139751548888896 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0604 23:57:46.238032 139751548888896 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 23:57:46.172209 139798385985344 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 23:57:46.214865 139798385985344 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 23:57:46.215547 139798385985344 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0604 23:57:46.215942 139798385985344 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0604 23:57:46.216002 139798385985344 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0604 23:57:46.218174 139798385985344 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 23:57:47.760129 139648147167040 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0604 23:57:47.760324 139648147167040 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 23:57:47.760728 139648147167040 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 23:57:47.761147 139648147167040 make_examples_core.py:301] Task 3/4: Found 3 candidate variants
I0604 23:57:47.761183 139648147167040 make_examples_core.py:301] Task 3/4: Created 5 examples
I0604 23:57:47.909702 139751548888896 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0604 23:57:47.910061 139751548888896 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 23:57:47.910834 139751548888896 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 23:57:47.911471 139751548888896 make_examples_core.py:301] Task 0/4: Found 3 candidate variants
I0604 23:57:47.911514 139751548888896 make_examples_core.py:301] Task 0/4: Created 5 examples
I0604 23:57:48.163161 139798385985344 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0604 23:57:48.163399 139798385985344 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 23:57:48.163865 139798385985344 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 23:57:48.164393 139798385985344 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0604 23:57:48.164426 139798385985344 make_examples_core.py:301] Task 1/4: Created 1 examples
I0604 23:57:48.479483 140051437832000 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0604 23:57:48.479843 140051437832000 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 23:57:48.480475 140051437832000 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 23:57:48.481458 140051437832000 make_examples_core.py:301] Task 2/4: Found 6 candidate variants
I0604 23:57:48.481543 140051437832000 make_examples_core.py:301] Task 2/4: Created 6 examples
real 0m5.371s
user 0m25.209s
sys 0m33.619s
***** 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 23:57:50.569181 140692313044800 call_variants.py:563] Total 1 writing processes started.
I0604 23:57:50.570499 140692313044800 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 23:57:50.570562 140692313044800 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0604 23:57:50.570801 140692313044800 call_variants.py:592] Use saved model: True
I0604 23:57:54.353434 140692313044800 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 23:57:54.353579 140692313044800 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 23:57:54.928680 140692313044800 call_variants.py:716] Predicted 17 examples in 1 batches [2.760 sec per 100].
I0604 23:57:54.995589 140692313044800 call_variants.py:779] Complete: call_variants.
real 0m7.006s
user 0m10.981s
sys 0m11.518s
***** 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"
I0604 23:57:57.416209 140642326402880 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-06-04 23:57:57.419950: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-04 23:57:57.420097: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 17
I0604 23:57:57.421154 140642326402880 postprocess_variants.py:1313] CVO sorting took 7.546742757161459e-05 minutes
I0604 23:57:57.421293 140642326402880 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0604 23:57:57.421323 140642326402880 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0604 23:57:57.439892 140642326402880 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0604 23:57:57.444995 140642326402880 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 4.3443838755289714e-05 minutes
I0604 23:57:57.531170 140642326402880 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0014343023300170898 minutes.
real 0m1.936s
user 0m4.982s
sys 0m9.544s
***** Running the command:*****
time /opt/deepvariant/bin/vcf_stats_report --input_vcf "HCC1395_BL.dv_rescue.vcf.gz" --outfile_base "HCC1395_BL.dv_rescue"
I0604 23:57:59.352667 139796537722688 genomics_reader.py:222] Reading HCC1395_BL.dv_rescue.vcf.gz with NativeVcfReader
real 0m1.891s
user 0m5.180s
sys 0m9.272s