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/fe/771bd61ead9c1a803a94a03a0b418c/.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/fe/771bd61ead9c1a803a94a03a0b418c/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/8cec261d5efbf269078e42e83159b5/Sig_18_Blood.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d9/8cec261d5efbf269078e42e83159b5/Sig_18_Blood.recalibrated.bam
==> STAGING COMPLETE (7 inputs)
2026-05-27 18:49:58.720385: 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.
I0527 18:50:00.158580 139766406719296 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
I0527 18:50:02.014871 140604985423680 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 18:50:02.021422 140604985423680 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
I0527 18:50:02.030088 140604985423680 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
I0527 18:50:02.004757 140167183566656 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 18:50:02.012138 140167183566656 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
I0527 18:50:02.021075 140167183566656 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
I0527 18:50:02.007522 140226417309504 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 18:50:02.014104 140226417309504 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
I0527 18:50:02.023067 140226417309504 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
I0527 18:50:02.010331 139698443024192 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 18:50:02.016816 139698443024192 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
I0527 18:50:02.025728 139698443024192 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 18:50:02.297309 140604985423680 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']
I0527 18:50:02.289093 140167183566656 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']
I0527 18:50:02.290970 140226417309504 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']
I0527 18:50:02.294530 139698443024192 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']
I0527 18:50:02.510947 140604985423680 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 18:50:02.500567 140167183566656 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 18:50:02.500931 140226417309504 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 18:50:02.506787 139698443024192 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 18:50:02.795577 140604985423680 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
I0527 18:50:02.837712 140604985423680 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 18:50:02.809033 140167183566656 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
I0527 18:50:02.850574 140167183566656 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 18:50:02.763875 140226417309504 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
I0527 18:50:02.805891 140226417309504 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
I0527 18:50:02.849252 140226417309504 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 18:50:02.849912 140226417309504 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0527 18:50:02.850375 140226417309504 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0527 18:50:02.850433 140226417309504 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0527 18:50:02.771056 139698443024192 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
I0527 18:50:02.815587 139698443024192 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
I0527 18:50:02.882050 140604985423680 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 18:50:02.882730 140604985423680 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0527 18:50:02.883198 140604985423680 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0527 18:50:02.883260 140604985423680 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0527 18:50:02.885486 140604985423680 make_examples_core.py:301] Task 3/4: 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
I0527 18:50:02.894644 140167183566656 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 18:50:02.895314 140167183566656 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0527 18:50:02.895766 140167183566656 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0527 18:50:02.895832 140167183566656 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0527 18:50:02.898362 140167183566656 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0527 18:50:02.853343 140226417309504 make_examples_core.py:301] Task 0/4: 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
I0527 18:50:02.859520 139698443024192 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 18:50:02.860170 139698443024192 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0527 18:50:02.860669 139698443024192 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0527 18:50:02.860742 139698443024192 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0527 18:50:02.862908 139698443024192 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0527 18:50:04.323648 139698443024192 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0527 18:50:04.323895 139698443024192 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 18:50:04.324376 139698443024192 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 18:50:04.324866 139698443024192 make_examples_core.py:301] Task 1/4: Found 2 candidate variants
I0527 18:50:04.324903 139698443024192 make_examples_core.py:301] Task 1/4: Created 2 examples
I0527 18:50:04.461928 140604985423680 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0527 18:50:04.462330 140604985423680 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 18:50:04.462940 140604985423680 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 18:50:04.463714 140604985423680 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0527 18:50:04.463771 140604985423680 make_examples_core.py:301] Task 3/4: Created 4 examples
I0527 18:50:05.344477 140167183566656 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0527 18:50:05.344945 140167183566656 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 18:50:05.345953 140167183566656 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 18:50:05.346720 140167183566656 make_examples_core.py:301] Task 2/4: Found 4 candidate variants
I0527 18:50:05.346780 140167183566656 make_examples_core.py:301] Task 2/4: Created 4 examples
I0527 18:50:06.421199 140226417309504 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0527 18:50:06.421447 140226417309504 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 18:50:06.421921 140226417309504 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 18:50:06.422428 140226417309504 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0527 18:50:06.422461 140226417309504 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m6.708s
user 0m27.278s
sys 0m31.036s
***** 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(
I0527 18:50:08.901986 139696383997760 call_variants.py:563] Total 1 writing processes started.
I0527 18:50:08.903602 139696383997760 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].
I0527 18:50:08.903667 139696383997760 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0527 18:50:08.903903 139696383997760 call_variants.py:592] Use saved model: True
I0527 18:50:12.904042 139696383997760 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].
I0527 18:50:12.904210 139696383997760 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].
I0527 18:50:13.491870 139696383997760 call_variants.py:716] Predicted 19 examples in 1 batches [2.517 sec per 100].
I0527 18:50:13.563710 139696383997760 call_variants.py:779] Complete: call_variants.
real 0m7.463s
user 0m11.486s
sys 0m11.769s
***** 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"
I0527 18:50:15.953604 140264860104512 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
2026-05-27 18:50:15.957271: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-05-27 18:50:15.957413: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 19
I0527 18:50:15.958348 140264860104512 postprocess_variants.py:1313] CVO sorting took 7.2022279103597e-05 minutes
I0527 18:50:15.958493 140264860104512 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0527 18:50:15.958522 140264860104512 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0527 18:50:15.978576 140264860104512 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
I0527 18:50:15.983950 140264860104512 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 4.7437349955240886e-05 minutes
I0527 18:50:16.077094 140264860104512 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0015505194664001466 minutes.
real 0m1.979s
user 0m4.988s
sys 0m9.568s
***** 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"
I0527 18:50:17.934282 140496838055744 genomics_reader.py:222] Reading germline_control_2.dv_rescue.vcf.gz with NativeVcfReader
real 0m1.910s
user 0m5.083s
sys 0m9.388s