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/ef/b672e8bdcc343a6f653734dd3cebda/.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/ef/b672e8bdcc343a6f653734dd3cebda/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/a19b5d9fae2acdd3f45de59d7ae393/Sig_18_Blood.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/af/a19b5d9fae2acdd3f45de59d7ae393/Sig_18_Blood.recalibrated.bam
==> STAGING COMPLETE (7 inputs)
2026-06-01 21:52:27.923086: 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.
I0601 21:52:29.303550 140478876337984 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
I0601 21:52:31.308746 140578535720768 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0601 21:52:31.322875 140578535720768 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
I0601 21:52:31.332228 140578535720768 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
I0601 21:52:31.349743 140490009175872 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0601 21:52:31.361456 140490009175872 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
I0601 21:52:31.370447 140490009175872 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
I0601 21:52:31.358601 139830499014464 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0601 21:52:31.370020 139830499014464 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
I0601 21:52:31.379138 139830499014464 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
I0601 21:52:31.397524 140635754719040 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0601 21:52:31.409190 140635754719040 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
I0601 21:52:31.418547 140635754719040 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0601 21:52:31.599899 140578535720768 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']
I0601 21:52:31.642454 140490009175872 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']
I0601 21:52:31.699213 140635754719040 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']
I0601 21:52:31.656583 139830499014464 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']
I0601 21:52:31.823750 140578535720768 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0601 21:52:31.886962 140490009175872 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0601 21:52:31.978440 140635754719040 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0601 21:52:31.962666 139830499014464 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0601 21:52:32.091327 140578535720768 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
I0601 21:52:32.133644 140578535720768 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
I0601 21:52:32.178204 140578535720768 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0601 21:52:32.178896 140578535720768 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0601 21:52:32.179404 140578535720768 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0601 21:52:32.179473 140578535720768 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0601 21:52:32.182075 140578535720768 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0601 21:52:32.158257 140490009175872 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
I0601 21:52:32.203768 140490009175872 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
I0601 21:52:32.248255 140490009175872 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0601 21:52:32.249023 140490009175872 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0601 21:52:32.249662 140490009175872 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0601 21:52:32.249765 140490009175872 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0601 21:52:32.252944 140490009175872 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0601 21:52:32.242395 140635754719040 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
I0601 21:52:32.251246 139830499014464 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
I0601 21:52:32.285622 140635754719040 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
I0601 21:52:32.330234 140635754719040 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0601 21:52:32.330961 140635754719040 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0601 21:52:32.331493 140635754719040 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0601 21:52:32.331566 140635754719040 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0601 21:52:32.334279 140635754719040 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0601 21:52:32.292064 139830499014464 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
I0601 21:52:32.336297 139830499014464 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0601 21:52:32.336986 139830499014464 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0601 21:52:32.337485 139830499014464 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0601 21:52:32.337555 139830499014464 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0601 21:52:32.339896 139830499014464 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0601 21:52:33.762455 140578535720768 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0601 21:52:33.762818 140578535720768 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0601 21:52:33.763395 140578535720768 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0601 21:52:33.764078 140578535720768 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0601 21:52:33.764122 140578535720768 make_examples_core.py:301] Task 3/4: Created 4 examples
I0601 21:52:33.795658 139830499014464 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0601 21:52:33.796048 139830499014464 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0601 21:52:33.797161 139830499014464 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0601 21:52:33.797889 139830499014464 make_examples_core.py:301] Task 1/4: Found 2 candidate variants
I0601 21:52:33.797936 139830499014464 make_examples_core.py:301] Task 1/4: Created 2 examples
I0601 21:52:34.365304 140490009175872 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0601 21:52:34.365729 140490009175872 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0601 21:52:34.366426 140490009175872 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0601 21:52:34.367261 140490009175872 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0601 21:52:34.367320 140490009175872 make_examples_core.py:301] Task 0/4: Created 9 examples
I0601 21:52:34.370027 140635754719040 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0601 21:52:34.370478 140635754719040 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0601 21:52:34.371441 140635754719040 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0601 21:52:34.372290 140635754719040 make_examples_core.py:301] Task 2/4: Found 4 candidate variants
I0601 21:52:34.372349 140635754719040 make_examples_core.py:301] Task 2/4: Created 4 examples
real 0m5.442s
user 0m30.147s
sys 0m40.160s
***** 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(
I0601 21:52:36.782683 139645785286464 call_variants.py:563] Total 1 writing processes started.
I0601 21:52:36.784364 139645785286464 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].
I0601 21:52:36.784432 139645785286464 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0601 21:52:36.784667 139645785286464 call_variants.py:592] Use saved model: True
I0601 21:52:41.270171 139645785286464 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].
I0601 21:52:41.270466 139645785286464 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].
I0601 21:52:42.068470 139645785286464 call_variants.py:716] Predicted 19 examples in 1 batches [3.446 sec per 100].
I0601 21:52:42.218380 139645785286464 call_variants.py:779] Complete: call_variants.
real 0m8.565s
user 0m12.903s
sys 0m18.427s
***** 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"
I0601 21:52:45.186494 140357982951232 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
2026-06-01 21:52:45.190522: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-01 21:52:45.190689: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 19
I0601 21:52:45.191686 140357982951232 postprocess_variants.py:1313] CVO sorting took 7.739067077636719e-05 minutes
I0601 21:52:45.191884 140357982951232 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0601 21:52:45.191928 140357982951232 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0601 21:52:45.213519 140357982951232 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
I0601 21:52:45.218908 140357982951232 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 4.509290059407552e-05 minutes
I0601 21:52:45.330607 140357982951232 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0018595059712727864 minutes.
real 0m2.337s
user 0m4.817s
sys 0m10.071s
***** 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"
I0601 21:52:47.662847 140277414893376 genomics_reader.py:222] Reading germline_control_2.dv_rescue.vcf.gz with NativeVcfReader
real 0m2.487s
user 0m4.502s
sys 0m10.686s