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/dd/0823236fd840685dac60e64234a76c/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/9b07206464e732a00b7bf74852ddd6/HCC1395_BL.recalibrated.bam
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/28/9b07206464e732a00b7bf74852ddd6/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/dd/0823236fd840685dac60e64234a76c/.command.run
==> STAGING COMPLETE (7 inputs)
2026-06-03 20:59:01.130043: 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.
***** 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 {}
I0603 20:59:02.444320 140439809734464 run_deepvariant.py:513] Creating a directory for intermediate results in tmp
I0603 20:59:04.299986 140473333434176 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0603 20:59:04.306819 140473333434176 make_examples_core.py:301] Task 2/4: Preparing inputs
I0603 20:59:04.315614 140473333434176 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0603 20:59:04.291629 140468825458496 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0603 20:59:04.299233 140468825458496 make_examples_core.py:301] Task 0/4: Preparing inputs
I0603 20:59:04.307969 140468825458496 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0603 20:59:04.402377 140212531001152 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0603 20:59:04.408889 140212531001152 make_examples_core.py:301] Task 3/4: Preparing inputs
I0603 20:59:04.417793 140212531001152 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0603 20:59:04.331804 140467118778176 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0603 20:59:04.338749 140467118778176 make_examples_core.py:301] Task 1/4: Preparing inputs
I0603 20:59:04.347694 140467118778176 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0603 20:59:04.682924 140212531001152 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']
I0603 20:59:04.585384 140473333434176 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']
I0603 20:59:04.622240 140467118778176 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']
I0603 20:59:04.578356 140468825458496 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']
I0603 20:59:04.795809 140473333434176 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0603 20:59:04.887869 140467118778176 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0603 20:59:04.793852 140468825458496 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0603 20:59:04.940294 140212531001152 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0603 20:59:05.068194 140473333434176 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
I0603 20:59:05.106010 140473333434176 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0603 20:59:05.063467 140468825458496 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
I0603 20:59:05.096699 140468825458496 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0603 20:59:05.210027 140212531001152 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
I0603 20:59:05.245096 140212531001152 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0603 20:59:05.288868 140212531001152 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0603 20:59:05.289527 140212531001152 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0603 20:59:05.289983 140212531001152 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0603 20:59:05.290048 140212531001152 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0603 20:59:05.292251 140212531001152 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0603 20:59:05.150623 140473333434176 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0603 20:59:05.151289 140473333434176 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0603 20:59:05.151805 140473333434176 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0603 20:59:05.151868 140473333434176 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0603 20:59:05.154387 140473333434176 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0603 20:59:05.160751 140467118778176 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
I0603 20:59:05.194547 140467118778176 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0603 20:59:05.238866 140467118778176 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0603 20:59:05.239603 140467118778176 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0603 20:59:05.240076 140467118778176 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0603 20:59:05.240149 140467118778176 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0603 20:59:05.242389 140467118778176 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0603 20:59:05.140314 140468825458496 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0603 20:59:05.140978 140468825458496 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0603 20:59:05.141424 140468825458496 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0603 20:59:05.141485 140468825458496 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0603 20:59:05.144434 140468825458496 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0603 20:59:06.832238 140212531001152 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0603 20:59:06.832488 140212531001152 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0603 20:59:06.833310 140212531001152 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0603 20:59:06.833779 140212531001152 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0603 20:59:06.833811 140212531001152 make_examples_core.py:301] Task 3/4: Created 4 examples
I0603 20:59:07.096317 140473333434176 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0603 20:59:07.096552 140473333434176 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0603 20:59:07.096971 140473333434176 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0603 20:59:07.097391 140473333434176 make_examples_core.py:301] Task 2/4: Found 6 candidate variants
I0603 20:59:07.097426 140473333434176 make_examples_core.py:301] Task 2/4: Created 6 examples
I0603 20:59:06.770147 140467118778176 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0603 20:59:06.770541 140467118778176 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0603 20:59:06.771571 140467118778176 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0603 20:59:06.772299 140467118778176 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0603 20:59:06.772344 140467118778176 make_examples_core.py:301] Task 1/4: Created 1 examples
I0603 20:59:07.976249 140468825458496 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0603 20:59:07.976488 140468825458496 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0603 20:59:07.976945 140468825458496 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0603 20:59:07.977442 140468825458496 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0603 20:59:07.977472 140468825458496 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m5.892s
user 0m21.001s
sys 0m22.194s
***** 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(
I0603 20:59:10.271937 140308721940288 call_variants.py:563] Total 1 writing processes started.
I0603 20:59:10.273578 140308721940288 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].
I0603 20:59:10.273655 140308721940288 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0603 20:59:10.273885 140308721940288 call_variants.py:592] Use saved model: True
I0603 20:59:14.534214 140308721940288 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].
I0603 20:59:14.534418 140308721940288 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].
I0603 20:59:15.149660 140308721940288 call_variants.py:716] Predicted 20 examples in 1 batches [2.487 sec per 100].
I0603 20:59:15.228884 140308721940288 call_variants.py:779] Complete: call_variants.
real 0m7.673s
user 0m11.813s
sys 0m11.510s
***** 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"
I0603 20:59:17.666612 140080356206400 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-06-03 20:59:17.670365: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-03 20:59:17.670521: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 20
I0603 20:59:17.671570 140080356206400 postprocess_variants.py:1313] CVO sorting took 7.507006327311198e-05 minutes
I0603 20:59:17.671728 140080356206400 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0603 20:59:17.671759 140080356206400 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0603 20:59:17.691990 140080356206400 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0603 20:59:17.697924 140080356206400 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 5.437135696411133e-05 minutes
I0603 20:59:17.787361 140080356206400 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0014879186948140463 minutes.
real 0m2.030s
user 0m5.020s
sys 0m9.605s
***** 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"
I0603 20:59:19.698444 140604536313664 genomics_reader.py:222] Reading germline_control_1.dv_rescue.vcf.gz with NativeVcfReader
real 0m1.952s
user 0m5.083s
sys 0m9.437s