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/21/c8c4e7a194461668a4973e157f4829/.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/e7/493cf948b1d450f8051fba2ea0097a/HCC1395_BL.recalibrated.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/493cf948b1d450f8051fba2ea0097a/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/21/c8c4e7a194461668a4973e157f4829/.command.run
==> STAGING COMPLETE (7 inputs)
2026-06-04 16:54:49.782374: 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.
I0604 16:54:51.145374 140275444881216 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
I0604 16:54:52.996631 140440260896576 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 16:54:53.008756 140440260896576 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
I0604 16:54:53.017357 140440260896576 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
I0604 16:54:53.014764 140157771679552 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
I0604 16:54:53.074197 139965873862464 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 16:54:53.085027 139965873862464 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
I0604 16:54:53.093627 139965873862464 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 16:54:53.025827 140157771679552 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
I0604 16:54:53.034642 140157771679552 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
I0604 16:54:53.111352 140228899616576 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 16:54:53.121920 140228899616576 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
I0604 16:54:53.130331 140228899616576 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 16:54:53.291721 140440260896576 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']
I0604 16:54:53.369654 139965873862464 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']
I0604 16:54:53.314804 140157771679552 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']
I0604 16:54:53.477357 140440260896576 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 16:54:53.498230 140157771679552 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 16:54:53.412001 140228899616576 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']
I0604 16:54:53.725174 140440260896576 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
I0604 16:54:53.763565 140440260896576 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
I0604 16:54:53.806832 140440260896576 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 16:54:53.807438 140440260896576 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0604 16:54:53.807844 140440260896576 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0604 16:54:53.807897 140440260896576 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0604 16:54:53.810309 140440260896576 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 16:54:53.597564 139965873862464 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 16:54:53.739861 140157771679552 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
I0604 16:54:53.785048 140157771679552 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
I0604 16:54:53.642486 140228899616576 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 16:54:53.832913 139965873862464 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
I0604 16:54:53.873415 139965873862464 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
I0604 16:54:53.916828 139965873862464 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 16:54:53.917405 139965873862464 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0604 16:54:53.917822 139965873862464 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0604 16:54:53.917871 139965873862464 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0604 16:54:53.920146 139965873862464 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 16:54:53.828359 140157771679552 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 16:54:53.828956 140157771679552 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0604 16:54:53.829390 140157771679552 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0604 16:54:53.829446 140157771679552 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0604 16:54:53.832297 140157771679552 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 16:54:53.872363 140228899616576 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
I0604 16:54:53.912349 140228899616576 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
I0604 16:54:53.954747 140228899616576 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 16:54:53.955326 140228899616576 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0604 16:54:53.955706 140228899616576 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0604 16:54:53.955755 140228899616576 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0604 16:54:53.957990 140228899616576 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 16:54:55.695934 140440260896576 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0604 16:54:55.696130 140440260896576 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 16:54:55.696530 140440260896576 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 16:54:55.696909 140440260896576 make_examples_core.py:301] Task 2/4: Found 6 candidate variants
I0604 16:54:55.696939 140440260896576 make_examples_core.py:301] Task 2/4: Created 6 examples
I0604 16:54:55.433588 139965873862464 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0604 16:54:55.433773 139965873862464 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 16:54:55.434483 139965873862464 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 16:54:55.434890 139965873862464 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0604 16:54:55.434922 139965873862464 make_examples_core.py:301] Task 3/4: Created 4 examples
I0604 16:54:55.444617 140228899616576 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0604 16:54:55.444813 140228899616576 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 16:54:55.445549 140228899616576 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 16:54:55.445964 140228899616576 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0604 16:54:55.445993 140228899616576 make_examples_core.py:301] Task 1/4: Created 1 examples
I0604 16:54:56.625368 140157771679552 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0604 16:54:56.625572 140157771679552 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 16:54:56.626003 140157771679552 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 16:54:56.626418 140157771679552 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0604 16:54:56.626452 140157771679552 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m5.769s
user 0m23.455s
sys 0m30.909s
***** 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(
I0604 16:54:58.682389 139642537187136 call_variants.py:563] Total 1 writing processes started.
I0604 16:54:58.683830 139642537187136 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].
I0604 16:54:58.683886 139642537187136 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0604 16:54:58.684082 139642537187136 call_variants.py:592] Use saved model: True
I0604 16:55:02.339652 139642537187136 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].
I0604 16:55:02.339827 139642537187136 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].
I0604 16:55:02.963954 139642537187136 call_variants.py:716] Predicted 20 examples in 1 batches [2.603 sec per 100].
I0604 16:55:03.034876 139642537187136 call_variants.py:779] Complete: call_variants.
real 0m6.941s
user 0m9.322s
sys 0m14.420s
***** 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"
I0604 16:55:05.468418 139659350751040 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-06-04 16:55:05.471855: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-04 16:55:05.471976: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 20
I0604 16:55:05.472887 139659350751040 postprocess_variants.py:1313] CVO sorting took 6.860097249348959e-05 minutes
I0604 16:55:05.472997 139659350751040 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0604 16:55:05.473024 139659350751040 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0604 16:55:05.491297 139659350751040 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0604 16:55:05.497013 139659350751040 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 5.413293838500977e-05 minutes
I0604 16:55:05.598021 139659350751040 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0016818483670552572 minutes.
real 0m1.921s
user 0m4.480s
sys 0m11.584s
***** 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"
I0604 16:55:07.421899 139994850383680 genomics_reader.py:222] Reading germline_control_1.dv_rescue.vcf.gz with NativeVcfReader
real 0m1.902s
user 0m4.222s
sys 0m11.803s