.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/12/9e4600fc4cb8d9544ed72808287c3e/.command.log
Size: 16.3 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-rnd-pltf-dev-nextflow-scratch-01/work/12/9e4600fc4cb8d9544ed72808287c3e/.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/12/9e4600fc4cb8d9544ed72808287c3e/.command.run
==> STAGING COMPLETE (7 inputs)

2026-06-08 20:42:52.948922: 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 20:42:54.380932 140289075590976 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 20:42:56.578248 139902984505152 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:42:56.613880 139902984505152 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 20:42:56.623168 139902984505152 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 20:42:56.578779 140157485508416 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:42:56.612868 140157485508416 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 20:42:56.623934 140157485508416 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
[W::hts_idx_load3] The index file is older than the data file: HCC1395_BL.recalibrated.bam.bai
I0608 20:42:56.834949 139750128850752 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:42:56.650224 140532988278592 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:42:56.680664 140532988278592 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 20:42:56.690346 140532988278592 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:42:57.015782 139902984505152 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 20:42:56.860200 139750128850752 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 20:42:56.874230 139750128850752 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:42:56.988270 140157485508416 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 20:42:57.067951 140532988278592 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 20:42:57.328302 139902984505152 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 20:42:57.259609 139750128850752 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 20:42:57.280285 140157485508416 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 20:42:57.613841 140157485508416 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 20:42:57.691242 139902984505152 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 20:42:57.794801 139902984505152 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 20:42:57.852019 139902984505152 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:42:57.852916 139902984505152 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0608 20:42:57.853508 139902984505152 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0608 20:42:57.853585 139902984505152 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 1 seconds
I0608 20:42:57.856407 139902984505152 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 20:42:57.668092 139750128850752 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.recalibrated.bam.bai
I0608 20:42:57.689806 140157485508416 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 20:42:57.751119 140157485508416 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:42:57.752455 140157485508416 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0608 20:42:57.753451 140157485508416 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0608 20:42:57.753530 140157485508416 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 1 seconds
I0608 20:42:57.756546 140157485508416 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 20:42:57.627391 140532988278592 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 20:42:58.083607 139750128850752 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 20:42:58.175884 139750128850752 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 20:42:58.243647 139750128850752 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:42:58.244457 139750128850752 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0608 20:42:58.244963 139750128850752 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0608 20:42:58.245048 139750128850752 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 1 seconds
I0608 20:42:58.247866 139750128850752 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 20:42:58.111482 140532988278592 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 20:42:58.208784 140532988278592 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 20:42:58.273630 140532988278592 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 20:42:58.274643 140532988278592 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0608 20:42:58.275380 140532988278592 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0608 20:42:58.275491 140532988278592 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 1 seconds
I0608 20:42:58.279154 140532988278592 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 20:43:00.455325 139750128850752 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0608 20:43:00.455755 139750128850752 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 20:43:00.456783 139750128850752 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 20:43:00.458097 139750128850752 make_examples_core.py:301] Task 3/4: Found 3 candidate variants
I0608 20:43:00.458209 139750128850752 make_examples_core.py:301] Task 3/4: Created 5 examples
I0608 20:43:00.205621 140157485508416 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0608 20:43:00.205879 140157485508416 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 20:43:00.206312 140157485508416 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 20:43:00.206802 140157485508416 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0608 20:43:00.206834 140157485508416 make_examples_core.py:301] Task 1/4: Created 1 examples
I0608 20:43:00.355169 140532988278592 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0608 20:43:00.355597 140532988278592 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 20:43:00.357128 140532988278592 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 20:43:00.358473 140532988278592 make_examples_core.py:301] Task 0/4: Found 3 candidate variants
I0608 20:43:00.358553 140532988278592 make_examples_core.py:301] Task 0/4: Created 5 examples
I0608 20:43:00.746527 139902984505152 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0608 20:43:00.746777 139902984505152 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 20:43:00.747233 139902984505152 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 20:43:00.747745 139902984505152 make_examples_core.py:301] Task 2/4: Found 6 candidate variants
I0608 20:43:00.747779 139902984505152 make_examples_core.py:301] Task 2/4: Created 6 examples

real	0m6.719s
user	0m31.316s
sys	0m43.584s

***** 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 20:43:03.081380 140186050557760 call_variants.py:563] Total 1 writing processes started.
I0608 20:43:03.083115 140186050557760 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 20:43:03.083192 140186050557760 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0608 20:43:03.083477 140186050557760 call_variants.py:592] Use saved model: True
I0608 20:43:07.627145 140186050557760 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 20:43:07.627387 140186050557760 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 20:43:08.677988 140186050557760 call_variants.py:716] Predicted 17 examples in 1 batches [5.471 sec per 100].
I0608 20:43:08.807433 140186050557760 call_variants.py:779] Complete: call_variants.

real	0m8.780s
user	0m10.364s
sys	0m16.610s

***** 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 20:43:11.611037 140372496271168 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-06-08 20:43:11.614809: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-08 20:43:11.614956: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 17
I0608 20:43:11.615971 140372496271168 postprocess_variants.py:1313] CVO sorting took 7.321039835611979e-05 minutes
I0608 20:43:11.616181 140372496271168 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0608 20:43:11.616212 140372496271168 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0608 20:43:11.640244 140372496271168 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0608 20:43:11.645310 140372496271168 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 3.670851389567057e-05 minutes
I0608 20:43:11.733335 140372496271168 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0014650464057922364 minutes.

real	0m2.099s
user	0m4.615s
sys	0m10.072s

***** 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 20:43:13.634952 139669692397376 genomics_reader.py:222] Reading HCC1395_BL.dv_rescue.vcf.gz with NativeVcfReader

real	0m1.925s
user	0m4.101s
sys	0m10.377s