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/9b/4a6acafb782086313db6b8b02f1ec4/.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-rnd-pltf-dev-nextflow-scratch-01/work/0e/1efc95d887ebdaf1c9892b5421119a/HCC1395_BL.recalibrated.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/1efc95d887ebdaf1c9892b5421119a/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/9b/4a6acafb782086313db6b8b02f1ec4/.command.run
==> STAGING COMPLETE (7 inputs)
2026-05-28 05:36:58.518748: 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.
I0528 05:36:59.771761 140615834044224 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 {}
I0528 05:37:01.554577 140672339756864 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 05:37:01.577429 140672339756864 make_examples_core.py:301] Task 0/4: Preparing inputs
I0528 05:37:01.586224 140672339756864 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 05:37:01.642743 139893696612160 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 05:37:01.674239 140651107084096 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 05:37:01.694268 140651107084096 make_examples_core.py:301] Task 3/4: Preparing inputs
I0528 05:37:01.702910 140651107084096 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 05:37:01.690465 140165456271168 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 05:37:01.709411 140165456271168 make_examples_core.py:301] Task 2/4: Preparing inputs
I0528 05:37:01.717828 140165456271168 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 05:37:01.663732 139893696612160 make_examples_core.py:301] Task 1/4: Preparing inputs
I0528 05:37:01.672662 139893696612160 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 05:37:01.967070 140651107084096 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']
I0528 05:37:01.848626 140672339756864 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']
I0528 05:37:01.981563 140165456271168 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']
I0528 05:37:01.937907 139893696612160 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']
I0528 05:37:02.170360 140651107084096 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0528 05:37:02.022901 140672339756864 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0528 05:37:02.190016 140165456271168 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0528 05:37:02.132645 139893696612160 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0528 05:37:02.417911 140651107084096 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
I0528 05:37:02.453708 140651107084096 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 05:37:02.254368 140672339756864 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
I0528 05:37:02.293237 140672339756864 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 05:37:02.337016 140672339756864 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 05:37:02.337666 140672339756864 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0528 05:37:02.338121 140672339756864 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0528 05:37:02.338172 140672339756864 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0528 05:37:02.340985 140672339756864 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0528 05:37:02.434019 140165456271168 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
I0528 05:37:02.378543 139893696612160 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
I0528 05:37:02.423228 139893696612160 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 05:37:02.497249 140651107084096 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 05:37:02.497875 140651107084096 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0528 05:37:02.498259 140651107084096 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0528 05:37:02.498316 140651107084096 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0528 05:37:02.500433 140651107084096 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0528 05:37:02.471019 140165456271168 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 05:37:02.514277 140165456271168 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 05:37:02.514934 140165456271168 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0528 05:37:02.515396 140165456271168 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0528 05:37:02.515470 140165456271168 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0528 05:37:02.517903 140165456271168 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0528 05:37:02.466420 139893696612160 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 05:37:02.467056 139893696612160 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0528 05:37:02.467518 139893696612160 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0528 05:37:02.467578 139893696612160 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0528 05:37:02.469794 139893696612160 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0528 05:37:04.015075 140651107084096 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0528 05:37:04.015247 140651107084096 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0528 05:37:04.015693 140651107084096 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0528 05:37:03.947730 139893696612160 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0528 05:37:03.948088 139893696612160 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0528 05:37:03.948725 139893696612160 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0528 05:37:03.949421 139893696612160 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0528 05:37:03.949468 139893696612160 make_examples_core.py:301] Task 1/4: Created 1 examples
I0528 05:37:04.016092 140651107084096 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0528 05:37:04.016122 140651107084096 make_examples_core.py:301] Task 3/4: Created 4 examples
I0528 05:37:04.431316 140165456271168 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0528 05:37:04.431538 140165456271168 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0528 05:37:04.431963 140165456271168 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0528 05:37:04.432410 140165456271168 make_examples_core.py:301] Task 2/4: Found 6 candidate variants
I0528 05:37:04.432440 140165456271168 make_examples_core.py:301] Task 2/4: Created 6 examples
I0528 05:37:05.101014 140672339756864 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0528 05:37:05.101180 140672339756864 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0528 05:37:05.101582 140672339756864 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0528 05:37:05.102013 140672339756864 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0528 05:37:05.102043 140672339756864 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m5.631s
user 0m26.762s
sys 0m42.020s
***** 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(
I0528 05:37:07.149817 139732020668224 call_variants.py:563] Total 1 writing processes started.
I0528 05:37:07.151142 139732020668224 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].
I0528 05:37:07.151203 139732020668224 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0528 05:37:07.151419 139732020668224 call_variants.py:592] Use saved model: True
I0528 05:37:11.076543 139732020668224 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].
I0528 05:37:11.076741 139732020668224 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].
I0528 05:37:11.987069 139732020668224 call_variants.py:716] Predicted 20 examples in 1 batches [3.954 sec per 100].
I0528 05:37:12.095425 139732020668224 call_variants.py:779] Complete: call_variants.
real 0m7.628s
user 0m9.247s
sys 0m17.001s
***** Running the command:*****
time /opt/deepvariant/bin/postprocess_variants --ref "Homo_sapiens_assembly38.fasta" --infile "tmp/call_variants_output.tfrecord.gz" --outfile "germline_control_1.dv_rescue.vcf.gz" --cpus "4" --gvcf_outfile "germline_control_1.dv_rescue.g.vcf.gz" --nonvariant_site_tfrecord_path "tmp/gvcf.tfrecord@4.gz"
I0528 05:37:14.631654 140279895967552 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-05-28 05:37:14.635131: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-05-28 05:37:14.635276: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 20
I0528 05:37:14.636213 140279895967552 postprocess_variants.py:1313] CVO sorting took 6.937583287556967e-05 minutes
I0528 05:37:14.636345 140279895967552 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0528 05:37:14.636373 140279895967552 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0528 05:37:14.655027 140279895967552 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0528 05:37:14.661039 140279895967552 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 6.0395399729410806e-05 minutes
I0528 05:37:14.749396 140279895967552 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0014691630999247233 minutes.
real 0m1.932s
user 0m4.291s
sys 0m10.216s
***** Running the command:*****
time /opt/deepvariant/bin/vcf_stats_report --input_vcf "germline_control_1.dv_rescue.vcf.gz" --outfile_base "germline_control_1.dv_rescue"
I0528 05:37:16.552375 139914764896064 genomics_reader.py:222] Reading germline_control_1.dv_rescue.vcf.gz with NativeVcfReader
real 0m1.870s
user 0m4.079s
sys 0m10.349s