***** 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
I0604 17:08:49.529280 139897697920832 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:08:49.543688 139897697920832 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
I0604 17:08:49.552228 139897697920832 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
I0604 17:08:49.529361 140593982965568 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:08:49.543674 140593982965568 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
I0604 17:08:49.552201 140593982965568 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
I0604 17:08:49.529193 139798510356288 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:08:49.543683 139798510356288 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
I0604 17:08:49.552289 139798510356288 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
I0604 17:08:49.579881 140643546965824 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:08:49.589993 140643546965824 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
I0604 17:08:49.598423 140643546965824 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:08:49.837004 139897697920832 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 17:08:49.834565 140593982965568 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']
I0604 17:08:49.884609 140643546965824 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 17:08:49.832559 139798510356288 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 17:08:50.079209 139897697920832 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:08:50.062127 140593982965568 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:08:50.045934 139798510356288 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:08:50.325984 139897697920832 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
I0604 17:08:50.366502 139897697920832 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:08:50.326568 140593982965568 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
I0604 17:08:50.366610 140593982965568 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:08:50.154577 140643546965824 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0604 17:08:50.297314 139798510356288 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
I0604 17:08:50.334854 139798510356288 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
I0604 17:08:50.409167 139897697920832 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:08:50.409780 139897697920832 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0604 17:08:50.410211 139897697920832 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0604 17:08:50.410267 139897697920832 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0604 17:08:50.412557 139897697920832 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: Sig_18_Blood.recalibrated.bam.bai
I0604 17:08:50.411406 140593982965568 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:08:50.412078 140593982965568 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0604 17:08:50.412433 140593982965568 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0604 17:08:50.412479 140593982965568 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0604 17:08:50.414758 140593982965568 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:08:50.425993 140643546965824 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
I0604 17:08:50.463746 140643546965824 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
I0604 17:08:50.510608 140643546965824 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:08:50.511229 140643546965824 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0604 17:08:50.511689 140643546965824 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0604 17:08:50.511749 140643546965824 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0604 17:08:50.514758 140643546965824 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: Sig_18_Blood.recalibrated.bam.bai
I0604 17:08:50.378871 139798510356288 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0604 17:08:50.379489 139798510356288 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0604 17:08:50.379911 139798510356288 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0604 17:08:50.379964 139798510356288 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0604 17:08:50.382508 139798510356288 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0604 17:08:51.803727 139897697920832 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0604 17:08:51.803926 139897697920832 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:08:51.804342 139897697920832 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:08:51.804736 139897697920832 make_examples_core.py:301] Task 1/4: Found 2 candidate variants
I0604 17:08:51.804768 139897697920832 make_examples_core.py:301] Task 1/4: Created 2 examples
I0604 17:08:51.989782 140593982965568 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0604 17:08:51.989984 140593982965568 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:08:51.990396 140593982965568 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:08:51.990787 140593982965568 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0604 17:08:51.990816 140593982965568 make_examples_core.py:301] Task 3/4: Created 4 examples
I0604 17:08:52.368588 139798510356288 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0604 17:08:52.368792 139798510356288 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:08:52.369193 139798510356288 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:08:52.369594 139798510356288 make_examples_core.py:301] Task 2/4: Found 4 candidate variants
I0604 17:08:52.369628 139798510356288 make_examples_core.py:301] Task 2/4: Created 4 examples
I0604 17:08:52.733889 140643546965824 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0604 17:08:52.734602 140643546965824 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0604 17:08:52.735445 140643546965824 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0604 17:08:52.736125 140643546965824 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0604 17:08:52.736174 140643546965824 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m5.399s
user 0m24.031s
sys 0m38.320s
***** 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 17:08:54.860574 140059046262592 call_variants.py:563] Total 1 writing processes started.
I0604 17:08:54.862095 140059046262592 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 17:08:54.862160 140059046262592 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0604 17:08:54.862362 140059046262592 call_variants.py:592] Use saved model: True
I0604 17:08:58.808318 140059046262592 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 17:08:58.808526 140059046262592 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 17:08:59.532441 140059046262592 call_variants.py:716] Predicted 19 examples in 1 batches [3.166 sec per 100].
I0604 17:08:59.619402 140059046262592 call_variants.py:779] Complete: call_variants.
real 0m7.344s
user 0m10.434s
sys 0m13.564s
***** 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"
I0604 17:09:02.136863 139783894628160 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
2026-06-04 17:09:02.140328: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-04 17:09:02.140458: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 19
I0604 17:09:02.141374 139783894628160 postprocess_variants.py:1313] CVO sorting took 6.821552912394206e-05 minutes
I0604 17:09:02.141536 139783894628160 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0604 17:09:02.141573 139783894628160 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0604 17:09:02.161480 139783894628160 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
I0604 17:09:02.166917 139783894628160 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 4.712740580240885e-05 minutes
I0604 17:09:02.266442 139783894628160 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.001656965414683024 minutes.
real 0m2.101s
user 0m4.462s
sys 0m11.784s
***** 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"
I0604 17:09:04.187895 140114920048448 genomics_reader.py:222] Reading germline_control_2.dv_rescue.vcf.gz with NativeVcfReader
real 0m1.996s
user 0m4.861s
sys 0m11.265s