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/17/7f25a52bca843a9d21007c9a8ac215/.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/17/7f25a52bca843a9d21007c9a8ac215/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/a990a08c35878a9f8edbfb86b22de5/Sig_18_Blood.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/94/a990a08c35878a9f8edbfb86b22de5/Sig_18_Blood.recalibrated.bam
==> STAGING COMPLETE (7 inputs)
2026-06-04 17:18:41.952613: 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 17:18:43.368952 140457533683520 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
I0604 17:18:45.299631 139710480557888 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:18:45.311412 139710480557888 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
I0604 17:18:45.320106 139710480557888 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
I0604 17:18:45.357206 139708052449088 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:18:45.367961 139708052449088 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
I0604 17:18:45.376651 139708052449088 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
I0604 17:18:45.372294 140564856153920 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:18:45.382793 140564856153920 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
I0604 17:18:45.391370 140564856153920 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
I0604 17:18:45.327003 140250399958848 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:18:45.338149 140250399958848 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
I0604 17:18:45.347074 140250399958848 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:18:45.598076 139710480557888 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 17:18:45.627456 140250399958848 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 17:18:45.811207 139710480557888 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:18:45.667676 139708052449088 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 17:18:45.667868 140564856153920 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 17:18:45.834927 140250399958848 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:18:46.056246 139710480557888 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 17:18:45.903154 139708052449088 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:18:45.947182 140564856153920 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0604 17:18:46.097619 139710480557888 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
I0604 17:18:46.141249 139710480557888 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:18:46.141961 139710480557888 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0604 17:18:46.142358 139710480557888 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0604 17:18:46.142409 139710480557888 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0604 17:18:46.144608 139710480557888 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:18:46.164513 139708052449088 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: Sig_18_Blood.recalibrated.bam.bai
I0604 17:18:46.203434 139708052449088 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
I0604 17:18:46.247026 139708052449088 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:18:46.247686 139708052449088 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0604 17:18:46.248131 139708052449088 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0604 17:18:46.248187 139708052449088 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0604 17:18:46.250908 139708052449088 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:18:46.223033 140564856153920 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
I0604 17:18:46.263543 140564856153920 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
I0604 17:18:46.307486 140564856153920 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:18:46.308097 140564856153920 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0604 17:18:46.308507 140564856153920 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0604 17:18:46.308560 140564856153920 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0604 17:18:46.311548 140564856153920 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:18:46.087451 140250399958848 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
I0604 17:18:46.131164 140250399958848 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
I0604 17:18:46.175006 140250399958848 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:18:46.175651 140250399958848 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0604 17:18:46.176136 140250399958848 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0604 17:18:46.176196 140250399958848 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0604 17:18:46.178480 140250399958848 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:18:47.540466 139710480557888 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0604 17:18:47.540682 139710480557888 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:18:47.541179 139710480557888 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:18:47.541619 139710480557888 make_examples_core.py:301] Task 1/4: Found 2 candidate variants
I0604 17:18:47.541651 139710480557888 make_examples_core.py:301] Task 1/4: Created 2 examples
I0604 17:18:47.745844 140250399958848 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0604 17:18:47.746065 140250399958848 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:18:47.746587 140250399958848 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:18:47.747024 140250399958848 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0604 17:18:47.747054 140250399958848 make_examples_core.py:301] Task 3/4: Created 4 examples
I0604 17:18:48.234017 139708052449088 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0604 17:18:48.234239 139708052449088 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:18:48.234726 139708052449088 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:18:48.235138 139708052449088 make_examples_core.py:301] Task 2/4: Found 4 candidate variants
I0604 17:18:48.235172 139708052449088 make_examples_core.py:301] Task 2/4: Created 4 examples
I0604 17:18:48.423513 140564856153920 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0604 17:18:48.423917 140564856153920 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:18:48.424773 140564856153920 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:18:48.425520 140564856153920 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0604 17:18:48.425573 140564856153920 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m5.415s
user 0m21.462s
sys 0m20.758s
***** 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 17:18:50.673137 140391510689600 call_variants.py:563] Total 1 writing processes started.
I0604 17:18:50.674522 140391510689600 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 17:18:50.674577 140391510689600 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0604 17:18:50.674776 140391510689600 call_variants.py:592] Use saved model: True
I0604 17:18:54.424653 140391510689600 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 17:18:54.424793 140391510689600 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 17:18:55.113652 140391510689600 call_variants.py:716] Predicted 19 examples in 1 batches [3.080 sec per 100].
I0604 17:18:55.194877 140391510689600 call_variants.py:779] Complete: call_variants.
real 0m7.254s
user 0m10.038s
sys 0m13.903s
***** 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"
I0604 17:18:57.857809 140243920832320 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
2026-06-04 17:18:57.861404: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-04 17:18:57.861561: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 19
I0604 17:18:57.862573 140243920832320 postprocess_variants.py:1313] CVO sorting took 7.151365280151367e-05 minutes
I0604 17:18:57.862735 140243920832320 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0604 17:18:57.862765 140243920832320 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0604 17:18:57.885395 140243920832320 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
I0604 17:18:57.890418 140243920832320 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 4.173517227172852e-05 minutes
I0604 17:18:57.993626 140243920832320 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0017183423042297363 minutes.
real 0m2.178s
user 0m4.813s
sys 0m11.508s
***** 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"
I0604 17:18:59.973858 140472230872896 genomics_reader.py:222] Reading germline_control_2.dv_rescue.vcf.gz with NativeVcfReader
real 0m2.041s
user 0m4.482s
sys 0m11.676s