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/4a/1d73470ef336ef9cca35734a018cbc/.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/4a/1d73470ef336ef9cca35734a018cbc/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/a2ccef1525a551970c21f9713564f9/Sig_18_Blood.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/a2ccef1525a551970c21f9713564f9/Sig_18_Blood.recalibrated.bam
==> STAGING COMPLETE (7 inputs)
2026-05-27 15:31:28.973535: 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.
I0527 15:31:30.235701 140497580578624 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
I0527 15:31:32.056051 140043157731136 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 15:31:32.062602 140043157731136 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
I0527 15:31:32.071295 140043157731136 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
I0527 15:31:32.031644 140665489430336 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 15:31:32.038991 140665489430336 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
I0527 15:31:32.047904 140665489430336 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
I0527 15:31:32.076144 140438400104256 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 15:31:32.082763 140438400104256 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
I0527 15:31:32.091490 140438400104256 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
I0527 15:31:32.051075 139834107762496 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 15:31:32.057776 139834107762496 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
I0527 15:31:32.066470 139834107762496 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 15:31:32.338694 140043157731136 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']
I0527 15:31:32.318411 140665489430336 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']
I0527 15:31:32.358827 140438400104256 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']
I0527 15:31:32.332474 139834107762496 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']
I0527 15:31:32.541900 140043157731136 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 15:31:32.510552 140665489430336 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 15:31:32.570494 140438400104256 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 15:31:32.524085 139834107762496 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 15:31:32.805513 140043157731136 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
I0527 15:31:32.842060 140043157731136 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
I0527 15:31:32.884924 140043157731136 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 15:31:32.885569 140043157731136 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0527 15:31:32.886009 140043157731136 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0527 15:31:32.886065 140043157731136 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0527 15:31:32.888233 140043157731136 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0527 15:31:32.772783 140665489430336 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
I0527 15:31:32.808722 140665489430336 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
I0527 15:31:32.851895 140665489430336 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 15:31:32.852532 140665489430336 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0527 15:31:32.853028 140665489430336 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0527 15:31:32.853091 140665489430336 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0527 15:31:32.855520 140665489430336 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0527 15:31:32.841563 140438400104256 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
I0527 15:31:32.877015 140438400104256 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
I0527 15:31:32.789547 139834107762496 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
I0527 15:31:32.828377 139834107762496 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
I0527 15:31:32.872030 139834107762496 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 15:31:32.872673 139834107762496 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0527 15:31:32.873156 139834107762496 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0527 15:31:32.873219 139834107762496 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0527 15:31:32.875351 139834107762496 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0527 15:31:32.920828 140438400104256 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 15:31:32.921514 140438400104256 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0527 15:31:32.921902 140438400104256 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0527 15:31:32.921959 140438400104256 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0527 15:31:32.924833 140438400104256 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0527 15:31:34.427571 140043157731136 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0527 15:31:34.427789 140043157731136 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 15:31:34.428226 140043157731136 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 15:31:34.428670 140043157731136 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0527 15:31:34.428704 140043157731136 make_examples_core.py:301] Task 3/4: Created 4 examples
I0527 15:31:34.284684 139834107762496 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0527 15:31:34.284871 139834107762496 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 15:31:34.285303 139834107762496 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 15:31:34.285730 139834107762496 make_examples_core.py:301] Task 1/4: Found 2 candidate variants
I0527 15:31:34.285760 139834107762496 make_examples_core.py:301] Task 1/4: Created 2 examples
I0527 15:31:34.831784 140665489430336 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0527 15:31:34.831969 140665489430336 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 15:31:34.832388 140665489430336 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 15:31:34.832837 140665489430336 make_examples_core.py:301] Task 2/4: Found 4 candidate variants
I0527 15:31:34.832870 140665489430336 make_examples_core.py:301] Task 2/4: Created 4 examples
I0527 15:31:35.006147 140438400104256 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0527 15:31:35.006509 140438400104256 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 15:31:35.007131 140438400104256 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 15:31:35.007849 140438400104256 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0527 15:31:35.007907 140438400104256 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m5.151s
user 0m24.509s
sys 0m32.030s
***** 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(
I0527 15:31:37.290875 140194598401856 call_variants.py:563] Total 1 writing processes started.
I0527 15:31:37.292371 140194598401856 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].
I0527 15:31:37.292428 140194598401856 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0527 15:31:37.292645 140194598401856 call_variants.py:592] Use saved model: True
I0527 15:31:41.087429 140194598401856 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].
I0527 15:31:41.087593 140194598401856 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].
I0527 15:31:41.704347 140194598401856 call_variants.py:716] Predicted 19 examples in 1 batches [2.678 sec per 100].
I0527 15:31:41.772662 140194598401856 call_variants.py:779] Complete: call_variants.
real 0m7.186s
user 0m11.602s
sys 0m11.246s
***** 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"
I0527 15:31:44.510971 140090329384768 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
2026-05-27 15:31:44.514666: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-05-27 15:31:44.514850: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 19
I0527 15:31:44.515919 140090329384768 postprocess_variants.py:1313] CVO sorting took 7.491509119669596e-05 minutes
I0527 15:31:44.516101 140090329384768 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0527 15:31:44.516134 140090329384768 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0527 15:31:44.544455 140090329384768 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
I0527 15:31:44.552904 140090329384768 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 8.082389831542969e-05 minutes
I0527 15:31:44.674522 140090329384768 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0020249128341674806 minutes.
real 0m2.468s
user 0m4.898s
sys 0m10.155s
***** 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"
I0527 15:31:46.943135 140256136218432 genomics_reader.py:222] Reading germline_control_2.dv_rescue.vcf.gz with NativeVcfReader
real 0m2.323s
user 0m4.822s
sys 0m10.008s