.command.log - Workdir - DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE (germline_control_1;germline_rescue_targets)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/36a4e8c61d9d2f8e92dfdbcc66db4b/.command.log
Size: 16.1 KB
Task: DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE (germline_control_1;germline_rescue_targets)
Attempt
Content

  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/e5/36a4e8c61d9d2f8e92dfdbcc66db4b/.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/98/a4798a32f5e9daf45b045790a1d26d/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/a4798a32f5e9daf45b045790a1d26d/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/e5/36a4e8c61d9d2f8e92dfdbcc66db4b/.command.run
==> STAGING COMPLETE (7 inputs)

2026-05-27 15:31:29.026367: 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 15:31:30.308063 140604168623936 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
I0527 15:31:32.139389 140313243182912 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 15:31:32.146920 140313243182912 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
I0527 15:31:32.155722 140313243182912 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
I0527 15:31:32.213814 139964052911936 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 15:31:32.220909 139964052911936 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
I0527 15:31:32.229735 139964052911936 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
I0527 15:31:32.210385 140499441669952 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 15:31:32.217121 140499441669952 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
I0527 15:31:32.225953 140499441669952 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
I0527 15:31:32.192741 139809627391808 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 15:31:32.199583 139809627391808 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
I0527 15:31:32.208395 139809627391808 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 15:31:32.494545 140499441669952 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 15:31:32.473509 139809627391808 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 15:31:32.426541 140313243182912 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 15:31:32.588762 139964052911936 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 15:31:32.723465 140499441669952 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 15:31:32.685776 139809627391808 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 15:31:32.611407 140313243182912 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 15:31:32.839897 139964052911936 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 15:31:32.985668 140499441669952 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
I0527 15:31:32.948150 139809627391808 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
I0527 15:31:32.984460 139809627391808 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 15:31:32.863642 140313243182912 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
I0527 15:31:32.899460 140313243182912 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
I0527 15:31:32.942818 140313243182912 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 15:31:32.943440 140313243182912 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0527 15:31:32.943892 140313243182912 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0527 15:31:32.943945 140313243182912 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0527 15:31:32.946802 140313243182912 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0527 15:31:33.094146 139964052911936 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
I0527 15:31:33.129578 139964052911936 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
I0527 15:31:33.173960 139964052911936 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 15:31:33.174616 139964052911936 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0527 15:31:33.175080 139964052911936 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0527 15:31:33.175134 139964052911936 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0527 15:31:33.177633 139964052911936 make_examples_core.py:301] Task 2/4: 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
I0527 15:31:33.020368 140499441669952 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
I0527 15:31:33.063588 140499441669952 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 15:31:33.064285 140499441669952 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0527 15:31:33.064795 140499441669952 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0527 15:31:33.064862 140499441669952 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0527 15:31:33.067080 140499441669952 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
I0527 15:31:33.028457 139809627391808 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 15:31:33.029133 139809627391808 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0527 15:31:33.029663 139809627391808 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0527 15:31:33.029731 139809627391808 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0527 15:31:33.031982 139809627391808 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0527 15:31:34.546419 139809627391808 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0527 15:31:34.546618 139809627391808 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 15:31:34.547048 139809627391808 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 15:31:34.547470 139809627391808 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0527 15:31:34.547501 139809627391808 make_examples_core.py:301] Task 3/4: Created 4 examples
I0527 15:31:34.603626 140499441669952 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0527 15:31:34.603965 140499441669952 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 15:31:34.604578 140499441669952 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 15:31:34.605230 140499441669952 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0527 15:31:34.605275 140499441669952 make_examples_core.py:301] Task 1/4: Created 1 examples
I0527 15:31:35.101007 139964052911936 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0527 15:31:35.101256 139964052911936 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 15:31:35.102067 139964052911936 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 15:31:35.102559 139964052911936 make_examples_core.py:301] Task 2/4: Found 6 candidate variants
I0527 15:31:35.102590 139964052911936 make_examples_core.py:301] Task 2/4: Created 6 examples
I0527 15:31:35.744329 140313243182912 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0527 15:31:35.744562 140313243182912 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 15:31:35.745010 140313243182912 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 15:31:35.745486 140313243182912 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0527 15:31:35.745516 140313243182912 make_examples_core.py:301] Task 0/4: Created 9 examples

real	0m5.751s
user	0m25.944s
sys	0m31.622s

***** 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 15:31:37.871639 140558931134272 call_variants.py:563] Total 1 writing processes started.
I0527 15:31:37.873024 140558931134272 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 15:31:37.873085 140558931134272 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0527 15:31:37.873288 140558931134272 call_variants.py:592] Use saved model: True
I0527 15:31:41.977255 140558931134272 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 15:31:41.977423 140558931134272 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 15:31:42.649165 140558931134272 call_variants.py:716] Predicted 20 examples in 1 batches [2.792 sec per 100].
I0527 15:31:42.726805 140558931134272 call_variants.py:779] Complete: call_variants.

real	0m7.470s
user	0m11.264s
sys	0m11.981s

***** 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"

I0527 15:31:45.552108 139675693217600 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-05-27 15:31:45.555931: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-05-27 15:31:45.556092: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 20
I0527 15:31:45.557128 139675693217600 postprocess_variants.py:1313] CVO sorting took 7.551113764444986e-05 minutes
I0527 15:31:45.557295 139675693217600 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0527 15:31:45.557326 139675693217600 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0527 15:31:45.574370 139675693217600 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0527 15:31:45.579320 139675693217600 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 4.095236460367839e-05 minutes
I0527 15:31:45.678285 139675693217600 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0016475399335225424 minutes.

real	0m2.408s
user	0m4.789s
sys	0m10.077s

***** 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"

I0527 15:31:47.957751 140231374714688 genomics_reader.py:222] Reading germline_control_1.dv_rescue.vcf.gz with NativeVcfReader

real	0m2.426s
user	0m5.176s
sys	0m9.783s