***** 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
I0603 21:45:56.336961 140208288216896 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0603 21:45:56.342279 140208288216896 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
I0603 21:45:56.357357 140208288216896 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
I0603 21:45:56.351916 139972794443584 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0603 21:45:56.356772 139972794443584 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
I0603 21:45:56.371412 139972794443584 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
I0603 21:45:56.363057 140105293190976 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0603 21:45:56.367920 140105293190976 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
I0603 21:45:56.382637 140105293190976 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
I0603 21:45:56.336808 140018342672192 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0603 21:45:56.342274 140018342672192 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
I0603 21:45:56.356976 140018342672192 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0603 21:45:56.898840 140208288216896 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']
I0603 21:45:56.912383 139972794443584 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']
I0603 21:45:56.929447 140105293190976 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']
I0603 21:45:56.896463 140018342672192 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']
I0603 21:45:57.255465 140208288216896 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0603 21:45:57.264241 139972794443584 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0603 21:45:57.278117 140105293190976 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0603 21:45:57.250938 140018342672192 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0603 21:45:57.703675 140208288216896 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
I0603 21:45:57.756994 140208288216896 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0603 21:45:57.712968 139972794443584 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
I0603 21:45:57.761951 139972794443584 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0603 21:45:57.726002 140105293190976 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
I0603 21:45:57.774270 140105293190976 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0603 21:45:57.697227 140018342672192 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
I0603 21:45:57.746775 140018342672192 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
I0603 21:45:57.846396 140208288216896 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0603 21:45:57.847294 140208288216896 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0603 21:45:57.847759 140208288216896 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0603 21:45:57.847830 140208288216896 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 1 seconds
I0603 21:45:57.851083 140208288216896 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: Sig_18_Blood.recalibrated.bam.bai
I0603 21:45:57.851780 139972794443584 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0603 21:45:57.852680 139972794443584 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0603 21:45:57.853176 139972794443584 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0603 21:45:57.853241 139972794443584 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 1 seconds
I0603 21:45:57.857587 139972794443584 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
I0603 21:45:57.866167 140105293190976 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0603 21:45:57.867045 140105293190976 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0603 21:45:57.867557 140105293190976 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0603 21:45:57.867622 140105293190976 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 1 seconds
I0603 21:45:57.871276 140105293190976 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: Sig_18_Blood.recalibrated.bam.bai
I0603 21:45:57.836367 140018342672192 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0603 21:45:57.837264 140018342672192 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0603 21:45:57.837756 140018342672192 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0603 21:45:57.837826 140018342672192 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 1 seconds
I0603 21:45:57.841042 140018342672192 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0603 21:46:00.636256 140208288216896 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0603 21:46:00.636387 140208288216896 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0603 21:46:00.636586 140208288216896 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0603 21:46:00.636915 140208288216896 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0603 21:46:00.636986 140208288216896 make_examples_core.py:301] Task 3/4: Created 4 examples
I0603 21:46:00.335855 140018342672192 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0603 21:46:00.335985 140018342672192 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0603 21:46:00.336201 140018342672192 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0603 21:46:00.336533 140018342672192 make_examples_core.py:301] Task 1/4: Found 2 candidate variants
I0603 21:46:00.336598 140018342672192 make_examples_core.py:301] Task 1/4: Created 2 examples
I0603 21:46:01.292930 140105293190976 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0603 21:46:01.293060 140105293190976 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0603 21:46:01.293256 140105293190976 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0603 21:46:01.293594 140105293190976 make_examples_core.py:301] Task 2/4: Found 4 candidate variants
I0603 21:46:01.293666 140105293190976 make_examples_core.py:301] Task 2/4: Created 4 examples
I0603 21:46:01.408903 139972794443584 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0603 21:46:01.409035 139972794443584 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0603 21:46:01.409243 139972794443584 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0603 21:46:01.409593 139972794443584 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0603 21:46:01.409674 139972794443584 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m8.370s
user 0m31.634s
sys 0m5.784s
***** 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(
I0603 21:46:04.745402 140059545532224 call_variants.py:563] Total 1 writing processes started.
I0603 21:46:04.747501 140059545532224 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].
I0603 21:46:04.747589 140059545532224 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0603 21:46:04.747841 140059545532224 call_variants.py:592] Use saved model: True
I0603 21:46:11.097790 140059545532224 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].
I0603 21:46:11.098037 140059545532224 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].
I0603 21:46:11.828965 140059545532224 call_variants.py:716] Predicted 19 examples in 1 batches [3.013 sec per 100].
I0603 21:46:11.903970 140059545532224 call_variants.py:779] Complete: call_variants.
real 0m11.004s
user 0m13.460s
sys 0m4.613s
***** 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"
I0603 21:46:15.500631 140582478559040 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
2026-06-03 21:46:15.506826: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-03 21:46:15.507039: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 19
I0603 21:46:15.508616 140582478559040 postprocess_variants.py:1313] CVO sorting took 0.00012207428614298502 minutes
I0603 21:46:15.508801 140582478559040 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0603 21:46:15.508858 140582478559040 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0603 21:46:15.531810 140582478559040 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
I0603 21:46:15.539420 140582478559040 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 5.7144959767659506e-05 minutes
I0603 21:46:15.676466 140582478559040 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0022817174593607586 minutes.
real 0m3.181s
user 0m5.418s
sys 0m3.852s
***** 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"
I0603 21:46:18.665354 139738153039680 genomics_reader.py:222] Reading germline_control_2.dv_rescue.vcf.gz with NativeVcfReader
real 0m3.116s
user 0m5.292s
sys 0m4.092s