***** 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
I0608 20:33:59.955775 140436584245056 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
I0608 20:33:59.931134 140573146007360 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:33:59.954210 140573146007360 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
I0608 20:33:59.963304 140573146007360 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:33:59.976556 140436584245056 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
I0608 20:33:59.985633 140436584245056 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
I0608 20:33:59.990118 140573510571840 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:34:00.011219 140573510571840 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
I0608 20:34:00.019965 140573510571840 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
I0608 20:33:59.997306 140703025420096 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:34:00.018176 140703025420096 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
I0608 20:34:00.026976 140703025420096 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:34:00.249726 140436584245056 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 20:34:00.284227 140573510571840 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 20:34:00.225520 140573146007360 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 20:34:00.290138 140703025420096 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 20:34:00.441761 140436584245056 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 20:34:00.495809 140573510571840 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 20:34:00.402214 140573146007360 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 20:34:00.507038 140703025420096 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0608 20:34:00.695457 140436584245056 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
I0608 20:34:00.772610 140436584245056 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:34:00.706127 140573146007360 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
I0608 20:34:00.777352 140573146007360 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:34:00.764093 140703025420096 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
I0608 20:34:00.816976 140436584245056 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:34:00.817683 140436584245056 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0608 20:34:00.818134 140436584245056 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0608 20:34:00.818191 140436584245056 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0608 20:34:00.820369 140436584245056 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 20:34:00.787346 140573510571840 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
I0608 20:34:00.853156 140573510571840 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
I0608 20:34:00.898434 140573510571840 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:34:00.899209 140573510571840 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0608 20:34:00.899740 140573510571840 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0608 20:34:00.899821 140573510571840 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0608 20:34:00.902909 140573510571840 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
I0608 20:34:00.823767 140573146007360 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:34:00.824503 140573146007360 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0608 20:34:00.825077 140573146007360 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0608 20:34:00.825154 140573146007360 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0608 20:34:00.827783 140573146007360 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
I0608 20:34:00.830267 140703025420096 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
I0608 20:34:00.874184 140703025420096 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0608 20:34:00.874922 140703025420096 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0608 20:34:00.875327 140703025420096 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0608 20:34:00.875390 140703025420096 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0608 20:34:00.877637 140703025420096 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0608 20:34:02.641285 140436584245056 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0608 20:34:02.641507 140436584245056 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 20:34:02.641934 140436584245056 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 20:34:02.642393 140436584245056 make_examples_core.py:301] Task 1/4: Found 2 candidate variants
I0608 20:34:02.642431 140436584245056 make_examples_core.py:301] Task 1/4: Created 2 examples
I0608 20:34:02.576013 140573146007360 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0608 20:34:02.576401 140573146007360 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 20:34:02.577416 140573146007360 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 20:34:02.578204 140573146007360 make_examples_core.py:301] Task 2/4: Found 4 candidate variants
I0608 20:34:02.578259 140573146007360 make_examples_core.py:301] Task 2/4: Created 4 examples
I0608 20:34:02.552875 140703025420096 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0608 20:34:02.553109 140703025420096 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 20:34:02.553539 140703025420096 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 20:34:02.553969 140703025420096 make_examples_core.py:301] Task 3/4: Found 1 candidate variants
I0608 20:34:02.554003 140703025420096 make_examples_core.py:301] Task 3/4: Created 1 examples
I0608 20:34:03.099173 140573510571840 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0608 20:34:03.099527 140573510571840 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0608 20:34:03.100043 140573510571840 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0608 20:34:03.100752 140573510571840 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0608 20:34:03.100809 140573510571840 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m5.359s
user 0m26.562s
sys 0m42.153s
***** 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 20:34:05.238451 140495301691200 call_variants.py:563] Total 1 writing processes started.
I0608 20:34:05.239910 140495301691200 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 20:34:05.239971 140495301691200 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0608 20:34:05.240211 140495301691200 call_variants.py:592] Use saved model: True
I0608 20:34:09.810588 140495301691200 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 20:34:09.810842 140495301691200 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 20:34:10.774045 140495301691200 call_variants.py:716] Predicted 16 examples in 1 batches [5.266 sec per 100].
I0608 20:34:10.879073 140495301691200 call_variants.py:779] Complete: call_variants.
real 0m8.603s
user 0m12.164s
sys 0m14.617s
***** Running the command:*****
time /opt/deepvariant/bin/postprocess_variants --ref "Homo_sapiens_assembly38.fasta" --infile "tmp/call_variants_output.tfrecord.gz" --outfile "Sig_18_Blood.dv_rescue.vcf.gz" --cpus "4" --gvcf_outfile "Sig_18_Blood.dv_rescue.g.vcf.gz" --nonvariant_site_tfrecord_path "tmp/gvcf.tfrecord@4.gz"
I0608 20:34:13.744595 140036422928192 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
2026-06-08 20:34:13.748327: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-08 20:34:13.748467: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 16
I0608 20:34:13.749493 140036422928192 postprocess_variants.py:1313] CVO sorting took 7.437467575073242e-05 minutes
I0608 20:34:13.749642 140036422928192 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0608 20:34:13.749672 140036422928192 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0608 20:34:13.772315 140036422928192 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
I0608 20:34:13.777565 140036422928192 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 4.602670669555664e-05 minutes
I0608 20:34:13.868022 140036422928192 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0015057643254597981 minutes.
real 0m2.071s
user 0m4.400s
sys 0m10.241s
***** Running the command:*****
time /opt/deepvariant/bin/vcf_stats_report --input_vcf "Sig_18_Blood.dv_rescue.vcf.gz" --outfile_base "Sig_18_Blood.dv_rescue"
I0608 20:34:15.841887 140346457790272 genomics_reader.py:222] Reading Sig_18_Blood.dv_rescue.vcf.gz with NativeVcfReader
real 0m2.059s
user 0m4.492s
sys 0m10.125s