.command.log - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE (HCC1395_BL;germline_rescue_targets)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/389c17b9e4508a48665fad724084db/.command.log
Size: 16.0 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE (HCC1395_BL;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-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/HCC1395_BL/HCC1395_BL.recal.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/13/389c17b9e4508a48665fad724084db/.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/13/389c17b9e4508a48665fad724084db/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/output_runs/dev_latest_regression_eks__47a821d--20260221-174447/preprocessing/recalibrated/HCC1395_BL/HCC1395_BL.recal.bam
==> STAGING COMPLETE (7 inputs)

2026-06-04 19:32:40.603519: 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 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
I0604 19:32:42.333889 140579762898752 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.recal.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.recal.bam.bai
I0604 19:32:44.709861 140309403080512 genomics_reader.py:222] Reading HCC1395_BL.recal.bam with NativeSamReader
I0604 19:32:44.717187 140309403080512 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.recal.bam.bai
I0604 19:32:44.729713 140309403080512 genomics_reader.py:222] Reading HCC1395_BL.recal.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recal.bam.bai
I0604 19:32:44.760480 139908437886784 genomics_reader.py:222] Reading HCC1395_BL.recal.bam with NativeSamReader
I0604 19:32:44.767045 139908437886784 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.recal.bam.bai
I0604 19:32:44.779241 139908437886784 genomics_reader.py:222] Reading HCC1395_BL.recal.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recal.bam.bai
I0604 19:32:44.797568 140257193686848 genomics_reader.py:222] Reading HCC1395_BL.recal.bam with NativeSamReader
I0604 19:32:44.804249 140257193686848 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.recal.bam.bai
I0604 19:32:44.816601 140257193686848 genomics_reader.py:222] Reading HCC1395_BL.recal.bam with NativeSamReader
I0604 19:32:45.141984 140309403080512 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']
I0604 19:32:45.179172 139908437886784 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']
I0604 19:32:45.225927 140257193686848 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']
I0604 19:32:45.435117 140309403080512 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recal.bam.bai
I0604 19:32:45.365960 140140251846464 genomics_reader.py:222] Reading HCC1395_BL.recal.bam with NativeSamReader
I0604 19:32:45.379130 140140251846464 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.recal.bam.bai
I0604 19:32:45.397107 140140251846464 genomics_reader.py:222] Reading HCC1395_BL.recal.bam with NativeSamReader
I0604 19:32:45.476745 139908437886784 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 19:32:45.554288 140257193686848 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 19:32:45.798357 140309403080512 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: HCC1395_BL.recal.bam.bai
I0604 19:32:45.855911 140309403080512 genomics_reader.py:222] Reading HCC1395_BL.recal.bam with NativeSamReader
I0604 19:32:45.841326 139908437886784 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.recal.bam.bai
I0604 19:32:45.926131 140309403080512 genomics_reader.py:222] Reading HCC1395_BL.recal.bam with NativeSamReader
I0604 19:32:45.926817 140309403080512 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0604 19:32:45.927297 140309403080512 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0604 19:32:45.927378 140309403080512 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 1 seconds
I0604 19:32:45.930630 140309403080512 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 19:32:46.042982 140140251846464 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']
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recal.bam.bai
I0604 19:32:45.902614 139908437886784 genomics_reader.py:222] Reading HCC1395_BL.recal.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recal.bam.bai
I0604 19:32:45.973066 139908437886784 genomics_reader.py:222] Reading HCC1395_BL.recal.bam with NativeSamReader
I0604 19:32:45.973750 139908437886784 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0604 19:32:45.974270 139908437886784 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0604 19:32:45.974342 139908437886784 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 1 seconds
I0604 19:32:45.978602 139908437886784 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 19:32:45.925575 140257193686848 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.recal.bam.bai
I0604 19:32:45.981901 140257193686848 genomics_reader.py:222] Reading HCC1395_BL.recal.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recal.bam.bai
I0604 19:32:46.053571 140257193686848 genomics_reader.py:222] Reading HCC1395_BL.recal.bam with NativeSamReader
I0604 19:32:46.054252 140257193686848 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0604 19:32:46.054788 140257193686848 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0604 19:32:46.054861 140257193686848 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 1 seconds
I0604 19:32:46.058458 140257193686848 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 19:32:46.461023 140140251846464 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 19:32:46.979352 140140251846464 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.recal.bam.bai
I0604 19:32:47.043641 140140251846464 genomics_reader.py:222] Reading HCC1395_BL.recal.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recal.bam.bai
I0604 19:32:47.153007 140140251846464 genomics_reader.py:222] Reading HCC1395_BL.recal.bam with NativeSamReader
I0604 19:32:47.154005 140140251846464 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0604 19:32:47.154681 140140251846464 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0604 19:32:47.154758 140140251846464 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 1 seconds
I0604 19:32:47.159944 140140251846464 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.01s elapsed]
I0604 19:32:48.736950 140309403080512 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0604 19:32:48.737186 140309403080512 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 19:32:48.737661 140309403080512 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 19:32:48.738161 140309403080512 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0604 19:32:48.738216 140309403080512 make_examples_core.py:301] Task 1/4: Created 1 examples
I0604 19:32:48.562142 139908437886784 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0604 19:32:48.562365 139908437886784 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 19:32:48.562829 139908437886784 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 19:32:48.563291 139908437886784 make_examples_core.py:301] Task 0/4: Found 3 candidate variants
I0604 19:32:48.563357 139908437886784 make_examples_core.py:301] Task 0/4: Created 3 examples
I0604 19:32:48.703534 140257193686848 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0604 19:32:48.703793 140257193686848 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 19:32:48.704541 140257193686848 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 19:32:48.705070 140257193686848 make_examples_core.py:301] Task 2/4: Found 4 candidate variants
I0604 19:32:48.705121 140257193686848 make_examples_core.py:301] Task 2/4: Created 4 examples
I0604 19:32:50.853165 140140251846464 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0604 19:32:50.853406 140140251846464 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 19:32:50.853883 140140251846464 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 19:32:50.854378 140140251846464 make_examples_core.py:301] Task 3/4: Found 1 candidate variants
I0604 19:32:50.854429 140140251846464 make_examples_core.py:301] Task 3/4: Created 1 examples

real	0m9.003s
user	0m30.524s
sys	0m26.055s

***** 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(
I0604 19:32:54.302804 139888215824192 call_variants.py:563] Total 1 writing processes started.
I0604 19:32:54.305085 139888215824192 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].
I0604 19:32:54.305183 139888215824192 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0604 19:32:54.305579 139888215824192 call_variants.py:592] Use saved model: True
I0604 19:32:59.793533 139888215824192 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].
I0604 19:32:59.793735 139888215824192 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].
I0604 19:33:00.950252 139888215824192 call_variants.py:716] Predicted 9 examples in 1 batches [11.335 sec per 100].
I0604 19:33:01.030069 139888215824192 call_variants.py:779] Complete: call_variants.

real	0m10.592s
user	0m11.231s
sys	0m9.725s

***** 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"

I0604 19:33:04.880840 140412828141376 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-06-04 19:33:04.889570: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-04 19:33:04.889729: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 9
I0604 19:33:04.891136 140412828141376 postprocess_variants.py:1313] CVO sorting took 0.0001514434814453125 minutes
I0604 19:33:04.891426 140412828141376 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0604 19:33:04.891466 140412828141376 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0604 19:33:04.917379 140412828141376 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0604 19:33:04.923403 140412828141376 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 4.264116287231445e-05 minutes
I0604 19:33:05.079030 140412828141376 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0025911649068196614 minutes.

real	0m3.644s
user	0m4.509s
sys	0m8.510s

***** Running the command:*****
time /opt/deepvariant/bin/vcf_stats_report --input_vcf "HCC1395_BL.dv_rescue.vcf.gz" --outfile_base "HCC1395_BL.dv_rescue"

I0604 19:33:08.432278 140622529451840 genomics_reader.py:222] Reading HCC1395_BL.dv_rescue.vcf.gz with NativeVcfReader

real	0m3.631s
user	0m4.359s
sys	0m8.857s