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/4f/52138fe270ba985f53329653a3b6d5/.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-rnd-pltf-dev-nextflow-scratch-01/work/d1/7fb75bb19bef014eecf269a038384b/HCC1395_BL.recalibrated.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/7fb75bb19bef014eecf269a038384b/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/4f/52138fe270ba985f53329653a3b6d5/.command.run
==> STAGING COMPLETE (7 inputs)
2026-06-04 17:18:41.989477: 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 17:18:43.303730 140701834159936 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 17:18:45.241608 140281181226816 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:18:45.254277 140281181226816 make_examples_core.py:301] Task 2/4: Preparing inputs
I0604 17:18:45.263069 140281181226816 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:18:45.248892 140467018692416 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:18:45.259691 140467018692416 make_examples_core.py:301] Task 3/4: Preparing inputs
I0604 17:18:45.268443 140467018692416 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:18:45.359816 140405756102464 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:18:45.543095 140281181226816 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 17:18:45.552138 140467018692416 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 17:18:45.378301 139719286560576 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:18:45.389142 139719286560576 make_examples_core.py:301] Task 1/4: Preparing inputs
I0604 17:18:45.397667 139719286560576 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:18:45.370637 140405756102464 make_examples_core.py:301] Task 0/4: Preparing inputs
I0604 17:18:45.379235 140405756102464 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:18:45.758022 140281181226816 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:18:45.755929 140467018692416 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:18:45.678377 139719286560576 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 17:18:45.663938 140405756102464 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 17:18:45.998050 140281181226816 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 17:18:45.994481 140467018692416 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 17:18:45.932413 139719286560576 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:18:45.932388 140405756102464 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:18:46.039402 140281181226816 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:18:46.083022 140281181226816 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:18:46.083686 140281181226816 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0604 17:18:46.084181 140281181226816 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0604 17:18:46.084247 140281181226816 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0604 17:18:46.086859 140281181226816 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:18:46.034386 140467018692416 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:18:46.078536 140467018692416 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:18:46.079150 140467018692416 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0604 17:18:46.079567 140467018692416 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0604 17:18:46.079622 140467018692416 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0604 17:18:46.082026 140467018692416 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:18:46.196693 139719286560576 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 17:18:46.237010 139719286560576 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:18:46.200291 140405756102464 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 17:18:46.236969 140405756102464 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:18:46.283971 139719286560576 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:18:46.284641 139719286560576 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0604 17:18:46.285061 139719286560576 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0604 17:18:46.285131 139719286560576 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0604 17:18:46.287523 139719286560576 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:18:46.281810 140405756102464 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:18:46.282490 140405756102464 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0604 17:18:46.282954 140405756102464 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0604 17:18:46.283018 140405756102464 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0604 17:18:46.286071 140405756102464 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:18:47.629618 140467018692416 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0604 17:18:47.629812 140467018692416 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:18:47.630213 140467018692416 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:18:47.630594 140467018692416 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0604 17:18:47.630628 140467018692416 make_examples_core.py:301] Task 3/4: Created 4 examples
I0604 17:18:47.843099 139719286560576 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0604 17:18:47.843502 139719286560576 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:18:47.844347 139719286560576 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:18:47.845052 139719286560576 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0604 17:18:47.845099 139719286560576 make_examples_core.py:301] Task 1/4: Created 1 examples
I0604 17:18:47.990505 140281181226816 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0604 17:18:47.991155 140281181226816 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:18:47.991826 140281181226816 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:18:47.992501 140281181226816 make_examples_core.py:301] Task 2/4: Found 6 candidate variants
I0604 17:18:47.992547 140281181226816 make_examples_core.py:301] Task 2/4: Created 6 examples
I0604 17:18:49.147152 140405756102464 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0604 17:18:49.147587 140405756102464 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:18:49.148532 140405756102464 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:18:49.149336 140405756102464 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0604 17:18:49.149396 140405756102464 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m6.167s
user 0m24.372s
sys 0m35.144s
***** 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 17:18:51.277111 139654303672128 call_variants.py:563] Total 1 writing processes started.
I0604 17:18:51.278575 139654303672128 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 17:18:51.278630 139654303672128 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0604 17:18:51.278829 139654303672128 call_variants.py:592] Use saved model: True
I0604 17:18:54.989492 139654303672128 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 17:18:54.989632 139654303672128 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 17:18:55.664516 139654303672128 call_variants.py:716] Predicted 20 examples in 1 batches [2.762 sec per 100].
I0604 17:18:55.736048 139654303672128 call_variants.py:779] Complete: call_variants.
real 0m7.175s
user 0m10.701s
sys 0m13.250s
***** Running the command:*****
time /opt/deepvariant/bin/postprocess_variants --ref "Homo_sapiens_assembly38.fasta" --infile "tmp/call_variants_output.tfrecord.gz" --outfile "germline_control_1.dv_rescue.vcf.gz" --cpus "4" --gvcf_outfile "germline_control_1.dv_rescue.g.vcf.gz" --nonvariant_site_tfrecord_path "tmp/gvcf.tfrecord@4.gz"
I0604 17:18:58.352494 140126584866624 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-06-04 17:18:58.356167: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-04 17:18:58.356303: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 20
I0604 17:18:58.357247 140126584866624 postprocess_variants.py:1313] CVO sorting took 7.135868072509766e-05 minutes
I0604 17:18:58.357406 140126584866624 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0604 17:18:58.357436 140126584866624 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0604 17:18:58.381338 140126584866624 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0604 17:18:58.388104 140126584866624 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 6.955862045288086e-05 minutes
I0604 17:18:58.490823 140126584866624 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.001710061232248942 minutes.
real 0m2.094s
user 0m4.441s
sys 0m11.799s
***** Running the command:*****
time /opt/deepvariant/bin/vcf_stats_report --input_vcf "germline_control_1.dv_rescue.vcf.gz" --outfile_base "germline_control_1.dv_rescue"
I0604 17:19:00.530344 140666842736448 genomics_reader.py:222] Reading germline_control_1.dv_rescue.vcf.gz with NativeVcfReader
real 0m2.098s
user 0m4.501s
sys 0m11.716s