.command.log - Workdir - DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE (germline_control_2;germline_rescue_targets)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/3f8adfacf79bd853c15f1cbb46456a/.command.log
Size: 16.2 KB
Task: DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE (germline_control_2;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/8e/3f8adfacf79bd853c15f1cbb46456a/.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/8e/3f8adfacf79bd853c15f1cbb46456a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/913060702caf09fcfc1e4e7b484246/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ae/913060702caf09fcfc1e4e7b484246/Sig_18_Blood.recalibrated.bam
==> STAGING COMPLETE (7 inputs)

2026-05-27 11:34:03.282224: 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 11:34:04.620014 139695989090112 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 "Sig_18_Blood.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: Sig_18_Blood.recalibrated.bam.bai
I0527 11:34:06.464862 139665227941696 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 11:34:06.471537 139665227941696 make_examples_core.py:301] Task 2/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0527 11:34:06.480391 139665227941696 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0527 11:34:06.451284 140409263781696 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 11:34:06.458004 140409263781696 make_examples_core.py:301] Task 0/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0527 11:34:06.466700 140409263781696 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0527 11:34:06.433607 139906037040960 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 11:34:06.440929 139906037040960 make_examples_core.py:301] Task 1/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0527 11:34:06.449710 139906037040960 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0527 11:34:06.460666 140506236417856 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 11:34:06.467431 140506236417856 make_examples_core.py:301] Task 3/4: Preparing inputs
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0527 11:34:06.476066 140506236417856 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 11:34:06.747243 139665227941696 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 11:34:06.734686 140409263781696 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 11:34:06.716966 139906037040960 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 11:34:06.744717 140506236417856 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 11:34:06.953791 139665227941696 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 11:34:06.928191 140409263781696 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 11:34:06.907410 139906037040960 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 11:34:06.939474 140506236417856 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 11:34:07.225509 139665227941696 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: Sig_18_Blood.recalibrated.bam.bai
I0527 11:34:07.261378 139665227941696 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0527 11:34:07.304996 139665227941696 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 11:34:07.305638 139665227941696 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0527 11:34:07.306008 139665227941696 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0527 11:34:07.306069 139665227941696 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0527 11:34:07.308496 139665227941696 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0527 11:34:07.192329 140409263781696 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: Sig_18_Blood.recalibrated.bam.bai
I0527 11:34:07.231075 140409263781696 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0527 11:34:07.275982 140409263781696 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 11:34:07.276654 140409263781696 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0527 11:34:07.277132 140409263781696 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0527 11:34:07.277191 140409263781696 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0527 11:34:07.280083 140409263781696 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0527 11:34:07.166104 139906037040960 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: Sig_18_Blood.recalibrated.bam.bai
I0527 11:34:07.203207 139906037040960 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0527 11:34:07.246875 139906037040960 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 11:34:07.247504 139906037040960 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0527 11:34:07.247964 139906037040960 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0527 11:34:07.248019 139906037040960 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0527 11:34:07.250213 139906037040960 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0527 11:34:07.201469 140506236417856 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: Sig_18_Blood.recalibrated.bam.bai
I0527 11:34:07.237787 140506236417856 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0527 11:34:07.281936 140506236417856 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0527 11:34:07.282610 140506236417856 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0527 11:34:07.283113 140506236417856 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0527 11:34:07.283177 140506236417856 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0527 11:34:07.285445 140506236417856 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0527 11:34:08.641698 139906037040960 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0527 11:34:08.641846 139906037040960 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 11:34:08.642220 139906037040960 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 11:34:08.642584 139906037040960 make_examples_core.py:301] Task 1/4: Found 2 candidate variants
I0527 11:34:08.642613 139906037040960 make_examples_core.py:301] Task 1/4: Created 2 examples
I0527 11:34:08.900385 139665227941696 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0527 11:34:08.900753 139665227941696 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 11:34:08.901335 139665227941696 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 11:34:08.901999 139665227941696 make_examples_core.py:301] Task 2/4: Found 3 candidate variants
I0527 11:34:08.902060 139665227941696 make_examples_core.py:301] Task 2/4: Created 3 examples
I0527 11:34:08.883366 140506236417856 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0527 11:34:08.883674 140506236417856 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 11:34:08.884156 140506236417856 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 11:34:08.884805 140506236417856 make_examples_core.py:301] Task 3/4: Found 2 candidate variants
I0527 11:34:08.884853 140506236417856 make_examples_core.py:301] Task 3/4: Created 2 examples
I0527 11:34:09.394517 140409263781696 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0527 11:34:09.394871 140409263781696 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 11:34:09.395361 140409263781696 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 11:34:09.396023 140409263781696 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0527 11:34:09.396094 140409263781696 make_examples_core.py:301] Task 0/4: Created 6 examples

real	0m5.123s
user	0m24.167s
sys	0m32.884s

***** 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 11:34:11.573588 139768785962816 call_variants.py:563] Total 1 writing processes started.
I0527 11:34:11.575037 139768785962816 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 11:34:11.575098 139768785962816 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0527 11:34:11.575302 139768785962816 call_variants.py:592] Use saved model: True
I0527 11:34:15.480992 139768785962816 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 11:34:15.481169 139768785962816 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 11:34:16.097675 139768785962816 call_variants.py:716] Predicted 13 examples in 1 batches [3.800 sec per 100].
I0527 11:34:16.165984 139768785962816 call_variants.py:779] Complete: call_variants.

real	0m7.176s
user	0m9.974s
sys	0m12.621s

***** Running the command:*****
time /opt/deepvariant/bin/postprocess_variants --ref "Homo_sapiens_assembly38.fasta" --infile "tmp/call_variants_output.tfrecord.gz" --outfile "germline_control_2.dv_rescue.vcf.gz" --cpus "4" --gvcf_outfile "germline_control_2.dv_rescue.g.vcf.gz" --nonvariant_site_tfrecord_path "tmp/gvcf.tfrecord@4.gz"

I0527 11:34:18.580629 140581962577728 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
2026-05-27 11:34:18.584336: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-05-27 11:34:18.584452: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 13
I0527 11:34:18.585430 140581962577728 postprocess_variants.py:1313] CVO sorting took 7.288058598836263e-05 minutes
I0527 11:34:18.585578 140581962577728 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0527 11:34:18.585607 140581962577728 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0527 11:34:18.604896 140581962577728 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
I0527 11:34:18.609645 140581962577728 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 3.869136174519857e-05 minutes
I0527 11:34:18.698513 140581962577728 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.001479323705037435 minutes.

real	0m1.998s
user	0m5.093s
sys	0m9.491s

***** Running the command:*****
time /opt/deepvariant/bin/vcf_stats_report --input_vcf "germline_control_2.dv_rescue.vcf.gz" --outfile_base "germline_control_2.dv_rescue"

I0527 11:34:20.572011 139946807383872 genomics_reader.py:222] Reading germline_control_2.dv_rescue.vcf.gz with NativeVcfReader

real	0m1.941s
user	0m5.129s
sys	0m9.372s