.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/9e/e42b0cf0407be2e0ea41c1f8c12803/.command.log
Size: 16.2 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/9e/e42b0cf0407be2e0ea41c1f8c12803/.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/9e/e42b0cf0407be2e0ea41c1f8c12803/.command.run
==> STAGING COMPLETE (7 inputs)

2026-05-28 21:13:32.861231: 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.
I0528 21:13:35.479839 140443969689408 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
I0528 21:13:38.440394 140480145147712 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 21:13:38.446630 140480145147712 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
I0528 21:13:38.460356 140480145147712 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
I0528 21:13:38.689692 140282468157248 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 21:13:38.697709 140282468157248 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
I0528 21:13:38.718394 140282468157248 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
I0528 21:13:38.533185 140473451292480 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 21:13:38.539030 140473451292480 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
I0528 21:13:38.552721 140473451292480 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
I0528 21:13:38.800884 140538120501056 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 21:13:38.806896 140538120501056 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
I0528 21:13:38.821045 140538120501056 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 21:13:38.970165 140473451292480 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']
I0528 21:13:38.862391 140480145147712 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']
I0528 21:13:39.176848 140282468157248 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']
I0528 21:13:39.234315 140538120501056 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']
I0528 21:13:39.330086 140473451292480 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0528 21:13:39.221837 140480145147712 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0528 21:13:39.602494 140282468157248 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0528 21:13:39.605063 140538120501056 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0528 21:13:39.761310 140473451292480 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
I0528 21:13:39.657447 140480145147712 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
I0528 21:13:39.746916 140480145147712 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 21:13:40.121466 140282468157248 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.recalibrated.bam.bai
I0528 21:13:40.210465 140282468157248 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 21:13:40.072102 140538120501056 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
I0528 21:13:40.159574 140538120501056 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
I0528 21:13:39.856303 140473451292480 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
I0528 21:13:39.957195 140473451292480 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 21:13:39.958173 140473451292480 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0528 21:13:39.958989 140473451292480 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0528 21:13:39.959116 140473451292480 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 1 seconds
I0528 21:13:39.962424 140473451292480 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
I0528 21:13:39.822499 140480145147712 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 21:13:39.823480 140480145147712 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0528 21:13:39.824194 140480145147712 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0528 21:13:39.824278 140480145147712 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 1 seconds
I0528 21:13:39.828423 140480145147712 make_examples_core.py:301] Task 0/4: 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
I0528 21:13:40.299655 140282468157248 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 21:13:40.300630 140282468157248 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0528 21:13:40.301425 140282468157248 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0528 21:13:40.301517 140282468157248 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 1 seconds
I0528 21:13:40.304772 140282468157248 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
I0528 21:13:40.236463 140538120501056 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0528 21:13:40.237395 140538120501056 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0528 21:13:40.238104 140538120501056 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0528 21:13:40.238183 140538120501056 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 1 seconds
I0528 21:13:40.241622 140538120501056 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0528 21:13:42.784641 140473451292480 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0528 21:13:42.784816 140473451292480 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0528 21:13:42.785042 140473451292480 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0528 21:13:42.785452 140473451292480 make_examples_core.py:301] Task 3/4: Found 3 candidate variants
I0528 21:13:42.785517 140473451292480 make_examples_core.py:301] Task 3/4: Created 5 examples
I0528 21:13:42.604521 140480145147712 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0528 21:13:42.604692 140480145147712 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0528 21:13:42.604907 140480145147712 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0528 21:13:42.605276 140480145147712 make_examples_core.py:301] Task 0/4: Found 3 candidate variants
I0528 21:13:42.605344 140480145147712 make_examples_core.py:301] Task 0/4: Created 5 examples
I0528 21:13:43.921291 140538120501056 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0528 21:13:43.921458 140538120501056 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0528 21:13:43.921676 140538120501056 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0528 21:13:43.922063 140538120501056 make_examples_core.py:301] Task 2/4: Found 6 candidate variants
I0528 21:13:43.922126 140538120501056 make_examples_core.py:301] Task 2/4: Created 6 examples
I0528 21:13:43.963222 140282468157248 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0528 21:13:43.963389 140282468157248 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0528 21:13:43.963609 140282468157248 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0528 21:13:43.963990 140282468157248 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0528 21:13:43.964049 140282468157248 make_examples_core.py:301] Task 1/4: Created 1 examples

real	0m9.186s
user	0m32.986s
sys	0m15.428s

***** 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(
I0528 21:13:47.901692 140086672803648 call_variants.py:563] Total 1 writing processes started.
I0528 21:13:47.904063 140086672803648 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].
I0528 21:13:47.904178 140086672803648 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0528 21:13:47.904544 140086672803648 call_variants.py:592] Use saved model: True
I0528 21:13:56.033302 140086672803648 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].
I0528 21:13:56.033581 140086672803648 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].
I0528 21:13:57.133049 140086672803648 call_variants.py:716] Predicted 17 examples in 1 batches [5.319 sec per 100].
I0528 21:13:57.230407 140086672803648 call_variants.py:779] Complete: call_variants.

real	0m13.958s
user	0m14.213s
sys	0m7.456s

***** 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"

I0528 21:14:02.054354 140595434075968 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-05-28 21:14:02.063802: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-05-28 21:14:02.064070: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 17
I0528 21:14:02.066083 140595434075968 postprocess_variants.py:1313] CVO sorting took 0.00017844041188557941 minutes
I0528 21:14:02.066487 140595434075968 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0528 21:14:02.066545 140595434075968 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0528 21:14:02.124307 140595434075968 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0528 21:14:02.132033 140595434075968 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 2.1831194559733072e-05 minutes
I0528 21:14:02.314569 140595434075968 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.003038179874420166 minutes.

real	0m4.448s
user	0m4.549s
sys	0m5.981s

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

I0528 21:14:06.708159 139999340705600 genomics_reader.py:222] Reading HCC1395_BL.dv_rescue.vcf.gz with NativeVcfReader

real	0m4.516s
user	0m4.775s
sys	0m5.753s