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/eb/fee4870b922712f750cb5399db2b33/.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/eb/fee4870b922712f750cb5399db2b33/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/8fc7f5716dfc4a815738382b6d56eb/Sig_18_Blood.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f1/8fc7f5716dfc4a815738382b6d56eb/Sig_18_Blood.recalibrated.bam
==> STAGING COMPLETE (7 inputs)
2026-06-05 20:52:35.162648: 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 20:52:36.447571 140394171844416 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
I0605 20:52:38.247041 139651065755456 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 20:52:38.257446 139651065755456 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
I0605 20:52:38.266067 139651065755456 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
I0605 20:52:38.231691 140432404064064 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 20:52:38.245879 140432404064064 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
I0605 20:52:38.254227 140432404064064 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
I0605 20:52:38.236912 140409358726976 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 20:52:38.248685 140409358726976 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
I0605 20:52:38.257150 140409358726976 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
I0605 20:52:38.231767 139962028631872 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 20:52:38.245872 139962028631872 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
I0605 20:52:38.254391 139962028631872 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 20:52:38.544274 139651065755456 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 20:52:38.529615 140432404064064 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 20:52:38.684632 140432404064064 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0605 20:52:38.536176 140409358726976 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 20:52:38.533778 139962028631872 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 20:52:38.708345 139651065755456 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0605 20:52:38.691874 140409358726976 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0605 20:52:38.686794 139962028631872 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0605 20:52:38.954712 139651065755456 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
I0605 20:52:38.991276 139651065755456 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
I0605 20:52:39.034469 139651065755456 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 20:52:39.035067 139651065755456 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0605 20:52:39.035473 139651065755456 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0605 20:52:39.035518 139651065755456 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0605 20:52:39.037887 139651065755456 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0605 20:52:38.913730 140432404064064 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
I0605 20:52:38.956675 140432404064064 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
I0605 20:52:38.999130 140432404064064 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 20:52:38.999722 140432404064064 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0605 20:52:39.000149 140432404064064 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0605 20:52:39.000194 140432404064064 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0605 20:52:39.003088 140432404064064 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0605 20:52:38.916838 140409358726976 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
I0605 20:52:38.958894 140409358726976 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
I0605 20:52:39.002155 140409358726976 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 20:52:39.002731 140409358726976 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0605 20:52:39.003139 140409358726976 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0605 20:52:39.003183 140409358726976 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0605 20:52:39.005708 140409358726976 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0605 20:52:38.910242 139962028631872 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
I0605 20:52:38.951338 139962028631872 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
I0605 20:52:38.994237 139962028631872 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 20:52:38.994813 139962028631872 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0605 20:52:38.995174 139962028631872 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0605 20:52:38.995218 139962028631872 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0605 20:52:38.997465 139962028631872 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0605 20:52:40.446230 139651065755456 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0605 20:52:40.446850 139651065755456 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0605 20:52:40.447556 139651065755456 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0605 20:52:40.448169 139651065755456 make_examples_core.py:301] Task 1/4: Found 2 candidate variants
I0605 20:52:40.448213 139651065755456 make_examples_core.py:301] Task 1/4: Created 2 examples
I0605 20:52:40.531280 139962028631872 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0605 20:52:40.531437 139962028631872 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0605 20:52:40.531798 139962028631872 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0605 20:52:40.532166 139962028631872 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0605 20:52:40.532195 139962028631872 make_examples_core.py:301] Task 3/4: Created 4 examples
I0605 20:52:41.037818 140432404064064 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0605 20:52:41.038001 140432404064064 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0605 20:52:41.038404 140432404064064 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0605 20:52:41.038800 140432404064064 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0605 20:52:41.038829 140432404064064 make_examples_core.py:301] Task 0/4: Created 9 examples
I0605 20:52:40.953390 140409358726976 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0605 20:52:40.953585 140409358726976 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0605 20:52:40.953981 140409358726976 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0605 20:52:40.954355 140409358726976 make_examples_core.py:301] Task 2/4: Found 4 candidate variants
I0605 20:52:40.954383 140409358726976 make_examples_core.py:301] Task 2/4: Created 4 examples
real 0m4.870s
user 0m22.734s
sys 0m38.387s
***** 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 20:52:43.104667 140140078114624 call_variants.py:563] Total 1 writing processes started.
I0605 20:52:43.106032 140140078114624 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 20:52:43.106095 140140078114624 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0605 20:52:43.106323 140140078114624 call_variants.py:592] Use saved model: True
I0605 20:52:46.757546 140140078114624 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 20:52:46.757687 140140078114624 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 20:52:47.393599 140140078114624 call_variants.py:716] Predicted 19 examples in 1 batches [2.816 sec per 100].
I0605 20:52:47.459500 140140078114624 call_variants.py:779] Complete: call_variants.
real 0m6.718s
user 0m9.549s
sys 0m13.745s
***** 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"
I0605 20:52:49.646543 140347530557248 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
2026-06-05 20:52:49.650093: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-05 20:52:49.650220: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 19
I0605 20:52:49.651159 140347530557248 postprocess_variants.py:1313] CVO sorting took 7.094542185465495e-05 minutes
I0605 20:52:49.651273 140347530557248 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0605 20:52:49.651301 140347530557248 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0605 20:52:49.669731 140347530557248 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
I0605 20:52:49.675430 140347530557248 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 5.247195561726888e-05 minutes
I0605 20:52:49.776741 140347530557248 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0016819556554158528 minutes.
real 0m1.921s
user 0m4.659s
sys 0m11.407s
***** 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"
I0605 20:52:51.559531 139730560788288 genomics_reader.py:222] Reading germline_control_2.dv_rescue.vcf.gz with NativeVcfReader
real 0m1.851s
user 0m4.636s
sys 0m11.345s