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/56/f98e50afc5ad5ab8c6f65b5c00612c/.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/56/f98e50afc5ad5ab8c6f65b5c00612c/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/b9327ccd07f95c93afdb2eed727086/Sig_18_Blood.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/b9327ccd07f95c93afdb2eed727086/Sig_18_Blood.recalibrated.bam
==> STAGING COMPLETE (7 inputs)
2026-06-08 22:19:16.494793: 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.
I0608 22:19:18.251143 139836273911616 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
I0608 22:19:20.735327 140371951400768 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 22:19:20.743389 140371951400768 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
I0608 22:19:20.673755 139999859214144 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 22:19:20.682864 139999859214144 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
I0608 22:19:20.694123 139999859214144 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
I0608 22:19:20.708081 140447289190208 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 22:19:20.718214 140447289190208 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
I0608 22:19:20.730216 140447289190208 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
I0608 22:19:20.754546 140371951400768 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
I0608 22:19:20.805647 140499143997248 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 22:19:20.814560 140499143997248 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
I0608 22:19:20.826001 140499143997248 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 22:19:21.094375 140371951400768 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']
I0608 22:19:21.038506 139999859214144 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']
I0608 22:19:21.076193 140447289190208 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']
I0608 22:19:21.174980 140499143997248 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']
I0608 22:19:21.387315 140371951400768 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 22:19:21.312123 139999859214144 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 22:19:21.412978 140447289190208 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 22:19:21.456996 140499143997248 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 22:19:21.733691 140371951400768 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
I0608 22:19:21.783698 140371951400768 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 22:19:21.646591 139999859214144 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
I0608 22:19:21.693205 139999859214144 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
I0608 22:19:21.748914 139999859214144 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 22:19:21.749811 139999859214144 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0608 22:19:21.750351 139999859214144 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0608 22:19:21.750421 139999859214144 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 1 seconds
I0608 22:19:21.753303 139999859214144 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 22:19:21.768591 140447289190208 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
I0608 22:19:21.818906 140447289190208 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 22:19:21.798626 140499143997248 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
I0608 22:19:21.837902 140371951400768 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 22:19:21.838729 140371951400768 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0608 22:19:21.839306 140371951400768 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0608 22:19:21.839377 140371951400768 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 1 seconds
I0608 22:19:21.842421 140371951400768 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
I0608 22:19:21.874069 140447289190208 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 22:19:21.874936 140447289190208 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0608 22:19:21.875429 140447289190208 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0608 22:19:21.875501 140447289190208 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 1 seconds
I0608 22:19:21.879379 140447289190208 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
I0608 22:19:21.847306 140499143997248 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
I0608 22:19:21.902378 140499143997248 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 22:19:21.903269 140499143997248 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0608 22:19:21.903789 140499143997248 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0608 22:19:21.903857 140499143997248 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 1 seconds
I0608 22:19:21.906742 140499143997248 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 22:19:23.692147 139999859214144 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0608 22:19:23.692574 139999859214144 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 22:19:23.693307 139999859214144 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 22:19:23.694157 139999859214144 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0608 22:19:23.694227 139999859214144 make_examples_core.py:301] Task 3/4: Created 4 examples
I0608 22:19:23.664417 140499143997248 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0608 22:19:23.664870 140499143997248 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 22:19:23.665566 140499143997248 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 22:19:23.666493 140499143997248 make_examples_core.py:301] Task 1/4: Found 2 candidate variants
I0608 22:19:23.666567 140499143997248 make_examples_core.py:301] Task 1/4: Created 2 examples
I0608 22:19:24.306900 140371951400768 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0608 22:19:24.307205 140371951400768 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 22:19:24.308025 140371951400768 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 22:19:24.308560 140371951400768 make_examples_core.py:301] Task 2/4: Found 4 candidate variants
I0608 22:19:24.308600 140371951400768 make_examples_core.py:301] Task 2/4: Created 4 examples
I0608 22:19:24.518440 140447289190208 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0608 22:19:24.518726 140447289190208 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 22:19:24.519400 140447289190208 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 22:19:24.519985 140447289190208 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0608 22:19:24.520029 140447289190208 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m6.791s
user 0m31.532s
sys 0m39.486s
***** 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(
I0608 22:19:27.899897 140437315766080 call_variants.py:563] Total 1 writing processes started.
I0608 22:19:27.902186 140437315766080 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].
I0608 22:19:27.902280 140437315766080 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0608 22:19:27.902587 140437315766080 call_variants.py:592] Use saved model: True
I0608 22:19:33.927127 140437315766080 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].
I0608 22:19:33.927346 140437315766080 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].
I0608 22:19:34.910775 140437315766080 call_variants.py:716] Predicted 19 examples in 1 batches [4.425 sec per 100].
I0608 22:19:35.029911 140437315766080 call_variants.py:779] Complete: call_variants.
real 0m11.109s
user 0m13.901s
sys 0m13.677s
***** 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"
I0608 22:19:38.348929 140683230873408 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
2026-06-08 22:19:38.353560: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-08 22:19:38.353730: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 19
I0608 22:19:38.354964 140683230873408 postprocess_variants.py:1313] CVO sorting took 9.036064147949219e-05 minutes
I0608 22:19:38.355172 140683230873408 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0608 22:19:38.355210 140683230873408 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0608 22:19:38.376086 140683230873408 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
I0608 22:19:38.382626 140683230873408 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 5.762179692586263e-05 minutes
I0608 22:19:38.504848 140683230873408 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0020342906316121417 minutes.
real 0m2.636s
user 0m5.536s
sys 0m11.252s
***** 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"
I0608 22:19:40.809044 140160720463680 genomics_reader.py:222] Reading germline_control_2.dv_rescue.vcf.gz with NativeVcfReader
real 0m2.375s
user 0m5.473s
sys 0m10.989s