***** 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 17:37:11.033497 140469620160320 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 17:37:11.044563 140469620160320 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 17:37:11.053662 140469620160320 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 17:37:11.050326 139974930704192 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 17:37:11.012993 139776547104576 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 17:37:11.026013 139776547104576 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 17:37:11.035152 139776547104576 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 17:37:11.062061 139974930704192 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 17:37:11.071352 139974930704192 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 17:37:11.098231 140670668584768 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 17:37:11.109977 140670668584768 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 17:37:11.118950 140670668584768 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 17:37:11.322138 140469620160320 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 17:37:11.342193 139974930704192 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 17:37:11.386569 140670668584768 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 17:37:11.303814 139776547104576 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 17:37:11.498149 140469620160320 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 17:37:11.536835 139974930704192 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 17:37:11.590948 140670668584768 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 17:37:11.475783 139776547104576 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 17:37:11.752786 140469620160320 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
I0608 17:37:11.794621 140469620160320 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 17:37:11.837681 140469620160320 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 17:37:11.838305 140469620160320 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0608 17:37:11.838808 140469620160320 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0608 17:37:11.838872 140469620160320 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0608 17:37:11.841121 140469620160320 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 17:37:11.785689 139974930704192 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 17:37:11.830595 139974930704192 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 17:37:11.720791 139776547104576 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 17:37:11.761959 139776547104576 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 17:37:11.805674 139776547104576 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 17:37:11.806277 139776547104576 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0608 17:37:11.806694 139776547104576 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0608 17:37:11.806744 139776547104576 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0608 17:37:11.809180 139776547104576 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
I0608 17:37:11.873512 139974930704192 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 17:37:11.874142 139974930704192 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0608 17:37:11.874648 139974930704192 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0608 17:37:11.874704 139974930704192 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0608 17:37:11.877629 139974930704192 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 17:37:11.893048 140670668584768 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 17:37:11.934476 140670668584768 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 17:37:11.978741 140670668584768 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0608 17:37:11.979425 140670668584768 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0608 17:37:11.980014 140670668584768 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0608 17:37:11.980086 140670668584768 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0608 17:37:11.982417 140670668584768 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 17:37:13.344892 140469620160320 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0608 17:37:13.345223 140469620160320 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 17:37:13.345762 140469620160320 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 17:37:13.346624 140469620160320 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0608 17:37:13.346681 140469620160320 make_examples_core.py:301] Task 1/4: Created 1 examples
I0608 17:37:13.741001 140670668584768 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0608 17:37:13.741466 140670668584768 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 17:37:13.742174 140670668584768 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 17:37:13.743015 140670668584768 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0608 17:37:13.743073 140670668584768 make_examples_core.py:301] Task 3/4: Created 4 examples
I0608 17:37:14.331332 139776547104576 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0608 17:37:14.331545 139776547104576 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 17:37:14.332012 139776547104576 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 17:37:14.332533 139776547104576 make_examples_core.py:301] Task 2/4: Found 6 candidate variants
I0608 17:37:14.332577 139776547104576 make_examples_core.py:301] Task 2/4: Created 6 examples
I0608 17:37:15.141197 139974930704192 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0608 17:37:15.141536 139974930704192 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 17:37:15.142078 139974930704192 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 17:37:15.142789 139974930704192 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0608 17:37:15.142851 139974930704192 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m6.327s
user 0m31.377s
sys 0m43.160s
***** 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 17:37:17.304818 139870048401216 call_variants.py:563] Total 1 writing processes started.
I0608 17:37:17.306281 139870048401216 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 17:37:17.306340 139870048401216 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0608 17:37:17.306581 139870048401216 call_variants.py:592] Use saved model: True
I0608 17:37:21.480706 139870048401216 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 17:37:21.480891 139870048401216 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 17:37:22.260766 139870048401216 call_variants.py:716] Predicted 20 examples in 1 batches [3.328 sec per 100].
I0608 17:37:22.382254 139870048401216 call_variants.py:779] Complete: call_variants.
real 0m8.090s
user 0m14.209s
sys 0m16.619s
***** 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"
I0608 17:37:25.266169 139701142349632 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-06-08 17:37:25.270004: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-08 17:37:25.270161: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 20
I0608 17:37:25.271293 139701142349632 postprocess_variants.py:1313] CVO sorting took 7.784366607666016e-05 minutes
I0608 17:37:25.271449 139701142349632 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0608 17:37:25.271491 139701142349632 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0608 17:37:25.292003 139701142349632 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0608 17:37:25.298380 139701142349632 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 6.376902262369791e-05 minutes
I0608 17:37:25.392803 139701142349632 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.001571504275004069 minutes.
real 0m2.219s
user 0m4.988s
sys 0m9.815s
***** 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"
I0608 17:37:27.508595 140177091508032 genomics_reader.py:222] Reading germline_control_1.dv_rescue.vcf.gz with NativeVcfReader
real 0m2.082s
user 0m5.315s
sys 0m9.325s