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/25/b4f7c2d9daf5c0d812af86aacc4bee/.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-rnd-pltf-dev-nextflow-scratch-01/work/ad/ded0dc28f0bedef0afd0b3c848896c/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/ded0dc28f0bedef0afd0b3c848896c/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/25/b4f7c2d9daf5c0d812af86aacc4bee/.command.run
==> STAGING COMPLETE (7 inputs)

2026-06-08 22:18:13.226466: 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 22:18:14.709232 140279009187648 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 22:18:16.810774 140683101087552 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 22:18:16.818694 140683101087552 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 22:18:16.829339 140683101087552 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 22:18:16.805565 140517371774784 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 22:18:16.815321 140517371774784 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 22:18:16.826045 140517371774784 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 22:18:16.805520 140646781335360 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 22:18:16.815317 140646781335360 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 22:18:16.826227 140646781335360 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 22:18:16.817723 140077654701888 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 22:18:16.825384 140077654701888 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 22:18:16.836010 140077654701888 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 22:18:17.177218 140683101087552 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 22:18:17.367723 140683101087552 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 22:18:17.166222 140517371774784 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 22:18:17.359585 140517371774784 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 22:18:17.165569 140646781335360 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 22:18:17.361623 140646781335360 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 22:18:17.183531 140077654701888 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 22:18:17.374524 140077654701888 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 22:18:17.639782 140683101087552 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
I0608 22:18:17.628770 140517371774784 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 22:18:17.632875 140646781335360 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 22:18:17.686453 140683101087552 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 22:18:17.739954 140683101087552 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 22:18:17.740651 140683101087552 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0608 22:18:17.741090 140683101087552 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0608 22:18:17.741145 140683101087552 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0608 22:18:17.743821 140683101087552 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: HCC1395_BL.recalibrated.bam.bai
I0608 22:18:17.673919 140517371774784 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 22:18:17.727307 140517371774784 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 22:18:17.727990 140517371774784 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0608 22:18:17.728420 140517371774784 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0608 22:18:17.728474 140517371774784 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0608 22:18:17.731018 140517371774784 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: HCC1395_BL.recalibrated.bam.bai
I0608 22:18:17.681159 140646781335360 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 22:18:17.735176 140646781335360 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 22:18:17.735903 140646781335360 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0608 22:18:17.736340 140646781335360 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0608 22:18:17.736395 140646781335360 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0608 22:18:17.739280 140646781335360 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 22:18:17.646823 140077654701888 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 22:18:17.688937 140077654701888 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 22:18:17.742066 140077654701888 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 22:18:17.742770 140077654701888 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0608 22:18:17.743198 140077654701888 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0608 22:18:17.743252 140077654701888 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0608 22:18:17.746671 140077654701888 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 22:18:19.647778 140683101087552 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0608 22:18:19.647976 140683101087552 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 22:18:19.648427 140683101087552 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 22:18:19.648905 140683101087552 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0608 22:18:19.648941 140683101087552 make_examples_core.py:301] Task 3/4: Created 4 examples
I0608 22:18:19.578916 140517371774784 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0608 22:18:19.579099 140517371774784 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 22:18:19.579520 140517371774784 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 22:18:19.579918 140517371774784 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0608 22:18:19.579957 140517371774784 make_examples_core.py:301] Task 1/4: Created 1 examples
I0608 22:18:20.117912 140646781335360 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0608 22:18:20.118112 140646781335360 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 22:18:20.118553 140646781335360 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 22:18:20.118969 140646781335360 make_examples_core.py:301] Task 2/4: Found 6 candidate variants
I0608 22:18:20.119006 140646781335360 make_examples_core.py:301] Task 2/4: Created 6 examples
I0608 22:18:21.175514 140077654701888 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0608 22:18:21.175748 140077654701888 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 22:18:21.176239 140077654701888 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 22:18:21.176719 140077654701888 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0608 22:18:21.176759 140077654701888 make_examples_core.py:301] Task 0/4: Created 9 examples

real	0m6.787s
user	0m28.969s
sys	0m36.285s

***** 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 22:18:23.567942 139739326609216 call_variants.py:563] Total 1 writing processes started.
I0608 22:18:23.569483 139739326609216 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 22:18:23.569550 139739326609216 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0608 22:18:23.569797 139739326609216 call_variants.py:592] Use saved model: True
I0608 22:18:28.127727 139739326609216 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 22:18:28.127923 139739326609216 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 22:18:28.754818 139739326609216 call_variants.py:716] Predicted 20 examples in 1 batches [2.510 sec per 100].
I0608 22:18:28.833243 139739326609216 call_variants.py:779] Complete: call_variants.

real	0m8.009s
user	0m12.158s
sys	0m12.910s

***** Running the command:*****
time /opt/deepvariant/bin/postprocess_variants --ref "Homo_sapiens_assembly38.fasta" --infile "tmp/call_variants_output.tfrecord.gz" --outfile "germline_control_1.dv_rescue.vcf.gz" --cpus "4" --gvcf_outfile "germline_control_1.dv_rescue.g.vcf.gz" --nonvariant_site_tfrecord_path "tmp/gvcf.tfrecord@4.gz"

I0608 22:18:31.417856 140173731301184 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-06-08 22:18:31.422290: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-08 22:18:31.422451: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 20
I0608 22:18:31.423654 140173731301184 postprocess_variants.py:1313] CVO sorting took 8.904139200846354e-05 minutes
I0608 22:18:31.423789 140173731301184 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0608 22:18:31.423825 140173731301184 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0608 22:18:31.441138 140173731301184 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0608 22:18:31.447138 140173731301184 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 5.005995432535807e-05 minutes
I0608 22:18:31.570867 140173731301184 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0020601868629455565 minutes.

real	0m2.291s
user	0m5.549s
sys	0m10.914s

***** Running the command:*****
time /opt/deepvariant/bin/vcf_stats_report --input_vcf "germline_control_1.dv_rescue.vcf.gz" --outfile_base "germline_control_1.dv_rescue"

I0608 22:18:33.687670 139765911316288 genomics_reader.py:222] Reading germline_control_1.dv_rescue.vcf.gz with NativeVcfReader

real	0m2.204s
user	0m5.377s
sys	0m10.948s