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/93/4c293f0a8fce0c6af89cbbc3d00e6b/.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-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam
Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/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/93/4c293f0a8fce0c6af89cbbc3d00e6b/.command.run
==> STAGING COMPLETE (7 inputs)
2026-06-08 20:33:56.718483: 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 20:33:58.115193 140027458930496 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 {}
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0608 20:34:00.004952 140506434074432 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0608 20:34:00.105206 139980875097920 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:34:00.124299 139980875097920 make_examples_core.py:301] Task 3/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0608 20:34:00.133004 139980875097920 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0608 20:34:00.076174 140319644759872 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:34:00.101597 140319644759872 make_examples_core.py:301] Task 2/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0608 20:34:00.110524 140319644759872 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0608 20:34:00.076743 140111610918720 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:34:00.101609 140111610918720 make_examples_core.py:301] Task 0/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0608 20:34:00.110466 140111610918720 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:34:00.031663 140506434074432 make_examples_core.py:301] Task 1/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0608 20:34:00.040628 140506434074432 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:34:00.306663 140506434074432 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 20:34:00.403405 139980875097920 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 20:34:00.373561 140319644759872 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']
I0608 20:34:00.375695 140111610918720 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 20:34:00.530769 140506434074432 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 20:34:00.643229 139980875097920 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 20:34:00.618225 140319644759872 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 20:34:00.632896 140111610918720 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 20:34:00.776181 140506434074432 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
I0608 20:34:00.901559 139980875097920 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: HCC1395_BL.recalibrated.bam.bai
I0608 20:34:00.966442 139980875097920 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0608 20:34:01.011233 139980875097920 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:34:01.012028 139980875097920 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0608 20:34:01.012512 139980875097920 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0608 20:34:01.012593 139980875097920 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0608 20:34:01.014972 139980875097920 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 20:34:00.879603 140319644759872 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: HCC1395_BL.recalibrated.bam.bai
I0608 20:34:00.953591 140319644759872 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0608 20:34:00.997398 140319644759872 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:34:00.998167 140319644759872 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0608 20:34:00.998650 140319644759872 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0608 20:34:00.998718 140319644759872 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0608 20:34:01.001323 140319644759872 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 20:34:00.895138 140111610918720 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: HCC1395_BL.recalibrated.bam.bai
I0608 20:34:00.962976 140111610918720 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0608 20:34:01.006855 140111610918720 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:34:01.007622 140111610918720 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0608 20:34:01.008068 140111610918720 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0608 20:34:01.008138 140111610918720 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0608 20:34:01.011094 140111610918720 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: HCC1395_BL.recalibrated.bam.bai
I0608 20:34:00.856058 140506434074432 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0608 20:34:00.899304 140506434074432 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:34:00.899998 140506434074432 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0608 20:34:00.900465 140506434074432 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0608 20:34:00.900521 140506434074432 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0608 20:34:00.902815 140506434074432 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 20:34:02.689815 139980875097920 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0608 20:34:02.690187 139980875097920 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 20:34:02.690797 139980875097920 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 20:34:02.691716 139980875097920 make_examples_core.py:301] Task 3/4: Found 3 candidate variants
I0608 20:34:02.691777 139980875097920 make_examples_core.py:301] Task 3/4: Created 5 examples
I0608 20:34:02.617193 140111610918720 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0608 20:34:02.617576 140111610918720 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 20:34:02.618179 140111610918720 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 20:34:02.619195 140111610918720 make_examples_core.py:301] Task 0/4: Found 3 candidate variants
I0608 20:34:02.619252 140111610918720 make_examples_core.py:301] Task 0/4: Created 5 examples
I0608 20:34:02.798406 140506434074432 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0608 20:34:02.798788 140506434074432 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 20:34:02.799392 140506434074432 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 20:34:02.800122 140506434074432 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0608 20:34:02.800174 140506434074432 make_examples_core.py:301] Task 1/4: Created 1 examples
I0608 20:34:03.275881 140319644759872 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0608 20:34:03.276576 140319644759872 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 20:34:03.277167 140319644759872 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 20:34:03.277899 140319644759872 make_examples_core.py:301] Task 2/4: Found 6 candidate variants
I0608 20:34:03.277955 140319644759872 make_examples_core.py:301] Task 2/4: Created 6 examples
real 0m5.495s
user 0m24.969s
sys 0m37.618s
***** 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 20:34:05.362161 139930874464064 call_variants.py:563] Total 1 writing processes started.
I0608 20:34:05.363493 139930874464064 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 20:34:05.363548 139930874464064 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0608 20:34:05.363765 139930874464064 call_variants.py:592] Use saved model: True
I0608 20:34:10.374256 139930874464064 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 20:34:10.374502 139930874464064 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 20:34:11.332046 139930874464064 call_variants.py:716] Predicted 17 examples in 1 batches [4.945 sec per 100].
I0608 20:34:11.458061 139930874464064 call_variants.py:779] Complete: call_variants.
real 0m8.900s
user 0m11.053s
sys 0m16.524s
***** Running the command:*****
time /opt/deepvariant/bin/postprocess_variants --ref "Homo_sapiens_assembly38.fasta" --infile "tmp/call_variants_output.tfrecord.gz" --outfile "HCC1395_BL.dv_rescue.vcf.gz" --cpus "4" --gvcf_outfile "HCC1395_BL.dv_rescue.g.vcf.gz" --nonvariant_site_tfrecord_path "tmp/gvcf.tfrecord@4.gz"
I0608 20:34:14.333854 140130175907648 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-06-08 20:34:14.337370: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-08 20:34:14.337509: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 17
I0608 20:34:14.338454 140130175907648 postprocess_variants.py:1313] CVO sorting took 6.916125615437825e-05 minutes
I0608 20:34:14.338624 140130175907648 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0608 20:34:14.338653 140130175907648 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0608 20:34:14.359839 140130175907648 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0608 20:34:14.364343 140130175907648 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 2.193450927734375e-05 minutes
I0608 20:34:14.453652 140130175907648 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0014865557352701823 minutes.
real 0m2.241s
user 0m4.308s
sys 0m10.499s
***** Running the command:*****
time /opt/deepvariant/bin/vcf_stats_report --input_vcf "HCC1395_BL.dv_rescue.vcf.gz" --outfile_base "HCC1395_BL.dv_rescue"
I0608 20:34:16.586830 140395576620864 genomics_reader.py:222] Reading HCC1395_BL.dv_rescue.vcf.gz with NativeVcfReader
real 0m2.162s
user 0m4.187s
sys 0m10.547s