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/a9/b86bdee0641d8875646bed76ada9fe/.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/a9/b86bdee0641d8875646bed76ada9fe/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/d477fe8b5b7c55927132efa2aa1068/Sig_18_Blood.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/d477fe8b5b7c55927132efa2aa1068/Sig_18_Blood.recalibrated.bam
==> STAGING COMPLETE (7 inputs)
2026-06-04 19:43:53.228540: 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 19:43:54.626986 139652795356992 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
I0604 19:43:56.507002 139671475210048 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 19:43:56.516267 139671475210048 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
I0604 19:43:56.507025 140138860746560 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 19:43:56.516226 140138860746560 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
I0604 19:43:56.507000 140212498609984 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 19:43:56.516265 140212498609984 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
I0604 19:43:56.507104 140174075520832 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 19:43:56.516230 140174075520832 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
I0604 19:43:56.524953 139671475210048 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
I0604 19:43:56.525026 140138860746560 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
I0604 19:43:56.524847 140212498609984 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
I0604 19:43:56.524775 140174075520832 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 19:43:56.791835 139671475210048 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 19:43:56.794336 140138860746560 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 19:43:56.789749 140212498609984 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 19:43:56.792437 140174075520832 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 19:43:57.033862 139671475210048 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 19:43:57.034980 140138860746560 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 19:43:57.022207 140212498609984 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 19:43:57.034701 140174075520832 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 19:43:57.303381 139671475210048 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 19:43:57.303388 140138860746560 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 19:43:57.318372 140212498609984 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 19:43:57.305906 140174075520832 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
I0604 19:43:57.336443 139671475210048 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
I0604 19:43:57.379415 139671475210048 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 19:43:57.380077 139671475210048 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0604 19:43:57.380564 139671475210048 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0604 19:43:57.380621 139671475210048 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0604 19:43:57.382869 139671475210048 make_examples_core.py:301] Task 3/4: 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
I0604 19:43:57.340145 140138860746560 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
I0604 19:43:57.383017 140138860746560 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 19:43:57.383670 140138860746560 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0604 19:43:57.384104 140138860746560 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0604 19:43:57.384167 140138860746560 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0604 19:43:57.386610 140138860746560 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
I0604 19:43:57.349504 140212498609984 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
I0604 19:43:57.392211 140212498609984 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 19:43:57.392847 140212498609984 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0604 19:43:57.393291 140212498609984 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0604 19:43:57.393352 140212498609984 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0604 19:43:57.396140 140212498609984 make_examples_core.py:301] Task 0/4: 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
I0604 19:43:57.340103 140174075520832 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
I0604 19:43:57.383566 140174075520832 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 19:43:57.384219 140174075520832 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0604 19:43:57.384631 140174075520832 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0604 19:43:57.384695 140174075520832 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0604 19:43:57.386859 140174075520832 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 19:43:58.789601 140174075520832 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0604 19:43:58.789829 140174075520832 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 19:43:58.790280 140174075520832 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 19:43:58.790731 140174075520832 make_examples_core.py:301] Task 1/4: Found 2 candidate variants
I0604 19:43:58.790765 140174075520832 make_examples_core.py:301] Task 1/4: Created 2 examples
I0604 19:43:58.919914 139671475210048 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0604 19:43:58.920167 139671475210048 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 19:43:58.920663 139671475210048 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 19:43:58.921129 139671475210048 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0604 19:43:58.921169 139671475210048 make_examples_core.py:301] Task 3/4: Created 4 examples
I0604 19:43:59.358124 140138860746560 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0604 19:43:59.358351 140138860746560 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 19:43:59.358784 140138860746560 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 19:43:59.359199 140138860746560 make_examples_core.py:301] Task 2/4: Found 4 candidate variants
I0604 19:43:59.359230 140138860746560 make_examples_core.py:301] Task 2/4: Created 4 examples
I0604 19:43:59.500437 140212498609984 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0604 19:43:59.500830 140212498609984 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 19:43:59.501506 140212498609984 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 19:43:59.502261 140212498609984 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0604 19:43:59.502315 140212498609984 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m5.245s
user 0m24.307s
sys 0m31.146s
***** 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 19:44:01.686594 140715097995072 call_variants.py:563] Total 1 writing processes started.
I0604 19:44:01.688032 140715097995072 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 19:44:01.688100 140715097995072 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0604 19:44:01.688294 140715097995072 call_variants.py:592] Use saved model: True
I0604 19:44:05.534116 140715097995072 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 19:44:05.534275 140715097995072 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 19:44:06.732701 140715097995072 call_variants.py:716] Predicted 19 examples in 1 batches [5.738 sec per 100].
I0604 19:44:06.815788 140715097995072 call_variants.py:779] Complete: call_variants.
real 0m8.222s
user 0m11.318s
sys 0m11.749s
***** 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"
I0604 19:44:09.854329 140105534637888 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
2026-06-04 19:44:09.861311: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-04 19:44:09.861463: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 19
I0604 19:44:09.862442 140105534637888 postprocess_variants.py:1313] CVO sorting took 0.00012156565984090169 minutes
I0604 19:44:09.862598 140105534637888 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0604 19:44:09.862629 140105534637888 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0604 19:44:09.882692 140105534637888 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
I0604 19:44:09.888097 140105534637888 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 4.783868789672852e-05 minutes
I0604 19:44:09.998629 140105534637888 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.001839752991994222 minutes.
real 0m2.202s
user 0m5.061s
sys 0m9.730s
***** 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"
I0604 19:44:12.496446 140308546152256 genomics_reader.py:222] Reading germline_control_2.dv_rescue.vcf.gz with NativeVcfReader
real 0m2.741s
user 0m5.517s
sys 0m9.733s