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/77/25fdfe4355161f01705a2e86973d74/.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/45/2c338fb82705e4e0b4e7a512d35d58/HCC1395_BL.recalibrated.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/2c338fb82705e4e0b4e7a512d35d58/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/77/25fdfe4355161f01705a2e86973d74/.command.run
==> STAGING COMPLETE (7 inputs)
2026-06-04 17:04:37.777805: 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 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
I0604 17:04:40.168697 139684720170816 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 {}
I0604 17:04:43.254880 140447595718464 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:04:43.261084 140447595718464 make_examples_core.py:301] Task 3/4: Preparing inputs
I0604 17:04:43.277376 140447595718464 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:04:43.254775 139703080482624 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:04:43.261086 139703080482624 make_examples_core.py:301] Task 1/4: Preparing inputs
I0604 17:04:43.277415 139703080482624 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:04:43.254856 139965735941952 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:04:43.261085 139965735941952 make_examples_core.py:301] Task 0/4: Preparing inputs
I0604 17:04:43.277334 139965735941952 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:04:43.254901 140326760920896 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:04:43.261089 140326760920896 make_examples_core.py:301] Task 2/4: Preparing inputs
I0604 17:04:43.277369 140326760920896 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:04:43.875147 140447595718464 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 17:04:43.875384 139703080482624 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 17:04:43.874020 139965735941952 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 17:04:43.870936 140326760920896 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 17:04:44.248450 140447595718464 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:04:44.253859 139703080482624 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:04:44.247352 139965735941952 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:04:44.245387 140326760920896 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:04:44.736733 140447595718464 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
I0604 17:04:44.791807 140447595718464 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:04:44.742402 139703080482624 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
I0604 17:04:44.791900 139703080482624 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:04:44.734629 139965735941952 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
I0604 17:04:44.784765 139965735941952 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:04:44.736527 140326760920896 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
I0604 17:04:44.791823 140326760920896 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:04:44.903925 140447595718464 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:04:44.904945 140447595718464 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0604 17:04:44.905489 140447595718464 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0604 17:04:44.905575 140447595718464 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 1 seconds
I0604 17:04:44.909200 140447595718464 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:04:44.899244 139703080482624 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:04:44.900241 139703080482624 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0604 17:04:44.900816 139703080482624 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0604 17:04:44.900897 139703080482624 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 1 seconds
I0604 17:04:44.904596 139703080482624 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:04:44.894958 139965735941952 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:04:44.895958 139965735941952 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0604 17:04:44.896499 139965735941952 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0604 17:04:44.896581 139965735941952 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 1 seconds
I0604 17:04:44.901701 139965735941952 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.01s elapsed]
I0604 17:04:44.897647 140326760920896 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0604 17:04:44.898624 140326760920896 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0604 17:04:44.899160 140326760920896 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0604 17:04:44.899241 140326760920896 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 1 seconds
I0604 17:04:44.903405 140326760920896 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:04:48.142228 140447595718464 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0604 17:04:48.142374 140447595718464 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:04:48.142602 140447595718464 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:04:48.142987 140447595718464 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0604 17:04:48.143056 140447595718464 make_examples_core.py:301] Task 3/4: Created 4 examples
I0604 17:04:48.085233 139703080482624 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0604 17:04:48.085366 139703080482624 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:04:48.085577 139703080482624 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:04:48.085935 139703080482624 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0604 17:04:48.086007 139703080482624 make_examples_core.py:301] Task 1/4: Created 1 examples
I0604 17:04:48.743376 140326760920896 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0604 17:04:48.743538 140326760920896 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:04:48.743756 140326760920896 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:04:48.744105 140326760920896 make_examples_core.py:301] Task 2/4: Found 6 candidate variants
I0604 17:04:48.744190 140326760920896 make_examples_core.py:301] Task 2/4: Created 6 examples
I0604 17:04:50.296361 139965735941952 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0604 17:04:50.296493 139965735941952 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:04:50.296705 139965735941952 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:04:50.297055 139965735941952 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0604 17:04:50.297124 139965735941952 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m10.636s
user 0m36.220s
sys 0m6.117s
***** 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 17:04:54.045123 140645364676416 call_variants.py:563] Total 1 writing processes started.
I0604 17:04:54.047481 140645364676416 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 17:04:54.047576 140645364676416 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0604 17:04:54.047869 140645364676416 call_variants.py:592] Use saved model: True
I0604 17:05:01.072726 140645364676416 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 17:05:01.072962 140645364676416 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 17:05:01.919557 140645364676416 call_variants.py:716] Predicted 20 examples in 1 batches [3.328 sec per 100].
I0604 17:05:02.000401 140645364676416 call_variants.py:779] Complete: call_variants.
real 0m12.277s
user 0m15.605s
sys 0m4.412s
***** 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 17:05:05.985238 140592121661248 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-06-04 17:05:05.991917: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-04 17:05:05.992152: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 20
I0604 17:05:05.993980 140592121661248 postprocess_variants.py:1313] CVO sorting took 0.00013315677642822266 minutes
I0604 17:05:05.994239 140592121661248 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0604 17:05:05.994290 140592121661248 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0604 17:05:06.019405 140592121661248 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0604 17:05:06.026322 140592121661248 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 2.7942657470703126e-05 minutes
I0604 17:05:06.178354 140592121661248 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0025293628374735513 minutes.
real 0m3.586s
user 0m5.915s
sys 0m4.170s
***** 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 17:05:09.566734 140205166298944 genomics_reader.py:222] Reading germline_control_1.dv_rescue.vcf.gz with NativeVcfReader
real 0m3.529s
user 0m6.280s
sys 0m3.910s