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/8d/d27c7620df962d6a68d744b8287bd2/.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/8d/d27c7620df962d6a68d744b8287bd2/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam.bai
Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam
==> STAGING COMPLETE (7 inputs)
2026-06-08 20:42:54.483136: 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.
I0608 20:42:56.345202 140312523228992 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
I0608 20:42:58.861991 140507110266688 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:42:58.887284 140507110266688 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
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0608 20:42:58.898376 140507110266688 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:42:58.891163 139807300876096 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:42:58.929524 139807300876096 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
I0608 20:42:58.943487 139807300876096 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
I0608 20:42:59.216250 140507110266688 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']
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0608 20:42:59.188505 140450215679808 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:42:59.212382 140450215679808 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
I0608 20:42:59.222178 140450215679808 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:42:59.326291 139807300876096 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']
I0608 20:42:59.124891 139786779105088 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:42:59.154966 139786779105088 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
I0608 20:42:59.168180 139786779105088 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:42:59.516627 140507110266688 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 20:42:59.651935 140450215679808 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']
I0608 20:42:59.541475 139786779105088 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']
I0608 20:42:59.830117 140507110266688 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
I0608 20:42:59.918577 140507110266688 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:42:59.823384 139807300876096 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 20:42:59.963670 139786779105088 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
I0608 20:42:59.970461 140507110266688 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:42:59.971282 140507110266688 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0608 20:42:59.971841 140507110266688 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0608 20:42:59.971920 140507110266688 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 1 seconds
I0608 20:42:59.974602 140507110266688 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 20:43:00.045635 140450215679808 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 20:43:00.206708 139807300876096 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
I0608 20:43:00.297780 139807300876096 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:43:00.343381 140450215679808 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
I0608 20:43:00.429714 140450215679808 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
I0608 20:43:00.479598 140450215679808 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:43:00.480438 140450215679808 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0608 20:43:00.481240 140450215679808 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0608 20:43:00.481308 140450215679808 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 1 seconds
I0608 20:43:00.484302 140450215679808 make_examples_core.py:301] Task 1/4: 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
I0608 20:43:00.352396 139807300876096 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:43:00.353225 139807300876096 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0608 20:43:00.353893 139807300876096 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0608 20:43:00.353981 139807300876096 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 1 seconds
I0608 20:43:00.358176 139807300876096 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 20:43:00.307035 139786779105088 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
I0608 20:43:00.392569 139786779105088 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
I0608 20:43:00.451727 139786779105088 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:43:00.452661 139786779105088 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0608 20:43:00.453601 139786779105088 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0608 20:43:00.453691 139786779105088 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 1 seconds
I0608 20:43:00.456847 139786779105088 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 20:43:01.806210 140507110266688 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0608 20:43:01.806636 140507110266688 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 20:43:01.807255 140507110266688 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 20:43:01.808168 140507110266688 make_examples_core.py:301] Task 2/4: Found 4 candidate variants
I0608 20:43:01.808230 140507110266688 make_examples_core.py:301] Task 2/4: Created 4 examples
I0608 20:43:02.179750 139786779105088 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0608 20:43:02.180013 139786779105088 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 20:43:02.180923 139786779105088 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 20:43:02.181703 139786779105088 make_examples_core.py:301] Task 3/4: Found 1 candidate variants
I0608 20:43:02.181755 139786779105088 make_examples_core.py:301] Task 3/4: Created 1 examples
I0608 20:43:02.376684 140450215679808 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0608 20:43:02.376836 140450215679808 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 20:43:02.377866 140450215679808 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 20:43:02.378557 140450215679808 make_examples_core.py:301] Task 1/4: Found 2 candidate variants
I0608 20:43:02.378608 140450215679808 make_examples_core.py:301] Task 1/4: Created 2 examples
I0608 20:43:02.813601 139807300876096 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0608 20:43:02.814096 139807300876096 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 20:43:02.815323 139807300876096 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 20:43:02.816415 139807300876096 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0608 20:43:02.816479 139807300876096 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m6.923s
user 0m29.932s
sys 0m41.848s
***** 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(
I0608 20:43:05.240192 140629520340800 call_variants.py:563] Total 1 writing processes started.
I0608 20:43:05.241866 140629520340800 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].
I0608 20:43:05.241934 140629520340800 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0608 20:43:05.242248 140629520340800 call_variants.py:592] Use saved model: True
I0608 20:43:09.600112 140629520340800 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].
I0608 20:43:09.600332 140629520340800 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].
I0608 20:43:10.644753 140629520340800 call_variants.py:716] Predicted 16 examples in 1 batches [5.719 sec per 100].
I0608 20:43:10.787248 140629520340800 call_variants.py:779] Complete: call_variants.
real 0m8.608s
user 0m10.808s
sys 0m17.619s
***** Running the command:*****
time /opt/deepvariant/bin/postprocess_variants --ref "Homo_sapiens_assembly38.fasta" --infile "tmp/call_variants_output.tfrecord.gz" --outfile "Sig_18_Blood.dv_rescue.vcf.gz" --cpus "4" --gvcf_outfile "Sig_18_Blood.dv_rescue.g.vcf.gz" --nonvariant_site_tfrecord_path "tmp/gvcf.tfrecord@4.gz"
I0608 20:43:13.560837 140589186918208 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
2026-06-08 20:43:13.564363: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-08 20:43:13.564491: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 16
I0608 20:43:13.565463 140589186918208 postprocess_variants.py:1313] CVO sorting took 6.976524988810222e-05 minutes
I0608 20:43:13.565619 140589186918208 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0608 20:43:13.565649 140589186918208 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0608 20:43:13.592097 140589186918208 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
I0608 20:43:13.597423 140589186918208 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 4.6988328297932945e-05 minutes
I0608 20:43:13.690762 140589186918208 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0015535632769266765 minutes.
real 0m2.036s
user 0m4.273s
sys 0m10.357s
***** Running the command:*****
time /opt/deepvariant/bin/vcf_stats_report --input_vcf "Sig_18_Blood.dv_rescue.vcf.gz" --outfile_base "Sig_18_Blood.dv_rescue"
I0608 20:43:15.628753 140655720335168 genomics_reader.py:222] Reading Sig_18_Blood.dv_rescue.vcf.gz with NativeVcfReader
real 0m1.999s
user 0m4.308s
sys 0m10.255s