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/fb/c47b048f9c8320db383fa53f5f46a8/.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/fb/c47b048f9c8320db383fa53f5f46a8/.command.run
==> STAGING COMPLETE (7 inputs)
2026-06-05 15:18:55.888571: 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.
I0605 15:18:57.375918 140138383542080 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 {}
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0605 15:18:59.339086 140004921870144 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 15:18:59.357372 140004921870144 make_examples_core.py:301] Task 1/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0605 15:18:59.367303 140004921870144 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0605 15:18:59.410497 139736163395392 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 15:18:59.421497 139736163395392 make_examples_core.py:301] Task 0/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0605 15:18:59.430737 139736163395392 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0605 15:18:59.339596 139705446127424 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 15:18:59.357028 139705446127424 make_examples_core.py:301] Task 2/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0605 15:18:59.367001 139705446127424 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0605 15:18:59.339484 139897111017280 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 15:18:59.357362 139897111017280 make_examples_core.py:301] Task 3/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0605 15:18:59.366814 139897111017280 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 15:18:59.636776 140004921870144 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']
I0605 15:18:59.634725 139705446127424 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']
I0605 15:18:59.636695 139897111017280 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']
I0605 15:18:59.699139 139736163395392 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']
I0605 15:18:59.853208 139705446127424 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0605 15:18:59.856383 139897111017280 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0605 15:18:59.950368 140004921870144 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0605 15:18:59.960804 139736163395392 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0605 15:19:00.239885 140004921870144 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: HCC1395_BL.recalibrated.bam.bai
I0605 15:19:00.313428 140004921870144 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 15:19:00.222445 139736163395392 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: HCC1395_BL.recalibrated.bam.bai
I0605 15:19:00.299661 139736163395392 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0605 15:19:00.344408 139736163395392 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 15:19:00.345088 139736163395392 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0605 15:19:00.345563 139736163395392 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0605 15:19:00.345625 139736163395392 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0605 15:19:00.348538 139736163395392 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0605 15:19:00.111725 139705446127424 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: HCC1395_BL.recalibrated.bam.bai
I0605 15:19:00.190916 139705446127424 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0605 15:19:00.235988 139705446127424 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 15:19:00.236778 139705446127424 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0605 15:19:00.237339 139705446127424 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0605 15:19:00.237437 139705446127424 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0605 15:19:00.240150 139705446127424 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0605 15:19:00.104327 139897111017280 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: HCC1395_BL.recalibrated.bam.bai
I0605 15:19:00.175314 139897111017280 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0605 15:19:00.219582 139897111017280 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 15:19:00.220290 139897111017280 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0605 15:19:00.220740 139897111017280 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0605 15:19:00.220795 139897111017280 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0605 15:19:00.223041 139897111017280 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: HCC1395_BL.recalibrated.bam.bai
I0605 15:19:00.358356 140004921870144 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 15:19:00.359126 140004921870144 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0605 15:19:00.359668 140004921870144 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0605 15:19:00.359752 140004921870144 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 1 seconds
I0605 15:19:00.362180 140004921870144 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0605 15:19:02.010828 139736163395392 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0605 15:19:02.011227 139736163395392 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0605 15:19:02.012243 139736163395392 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0605 15:19:02.013042 139736163395392 make_examples_core.py:301] Task 0/4: Found 3 candidate variants
I0605 15:19:02.013102 139736163395392 make_examples_core.py:301] Task 0/4: Created 5 examples
I0605 15:19:01.912957 139897111017280 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0605 15:19:01.913192 139897111017280 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0605 15:19:01.913645 139897111017280 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0605 15:19:01.914093 139897111017280 make_examples_core.py:301] Task 3/4: Found 3 candidate variants
I0605 15:19:01.914128 139897111017280 make_examples_core.py:301] Task 3/4: Created 5 examples
I0605 15:19:02.339157 140004921870144 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0605 15:19:02.339605 140004921870144 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0605 15:19:02.341030 140004921870144 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0605 15:19:02.341867 140004921870144 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0605 15:19:02.341922 140004921870144 make_examples_core.py:301] Task 1/4: Created 1 examples
I0605 15:19:02.624502 139705446127424 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0605 15:19:02.624742 139705446127424 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0605 15:19:02.625187 139705446127424 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0605 15:19:02.625642 139705446127424 make_examples_core.py:301] Task 2/4: Found 6 candidate variants
I0605 15:19:02.625674 139705446127424 make_examples_core.py:301] Task 2/4: Created 6 examples
real 0m5.596s
user 0m29.671s
sys 0m38.043s
***** 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(
I0605 15:19:04.990193 140438865487680 call_variants.py:563] Total 1 writing processes started.
I0605 15:19:04.991832 140438865487680 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].
I0605 15:19:04.991913 140438865487680 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0605 15:19:04.992185 140438865487680 call_variants.py:592] Use saved model: True
I0605 15:19:09.518323 140438865487680 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].
I0605 15:19:09.518527 140438865487680 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].
I0605 15:19:10.644403 140438865487680 call_variants.py:716] Predicted 17 examples in 1 batches [5.848 sec per 100].
I0605 15:19:10.787589 140438865487680 call_variants.py:779] Complete: call_variants.
real 0m8.620s
user 0m12.937s
sys 0m17.252s
***** 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"
I0605 15:19:13.370103 140368976717632 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-06-05 15:19:13.373933: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-05 15:19:13.374076: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 17
I0605 15:19:13.375049 140368976717632 postprocess_variants.py:1313] CVO sorting took 7.434686024983724e-05 minutes
I0605 15:19:13.375240 140368976717632 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0605 15:19:13.375272 140368976717632 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0605 15:19:13.397969 140368976717632 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0605 15:19:13.404096 140368976717632 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 5.865891774495443e-05 minutes
I0605 15:19:13.501285 140368976717632 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0016178250312805175 minutes.
real 0m2.165s
user 0m5.163s
sys 0m9.588s
***** Running the command:*****
time /opt/deepvariant/bin/vcf_stats_report --input_vcf "HCC1395_BL.dv_rescue.vcf.gz" --outfile_base "HCC1395_BL.dv_rescue"
I0605 15:19:15.508480 140685142943552 genomics_reader.py:222] Reading HCC1395_BL.dv_rescue.vcf.gz with NativeVcfReader
real 0m2.042s
user 0m5.207s
sys 0m9.395s