***** 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
I0605 14:00:29.761522 140527781259072 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
I0605 14:00:29.761216 139659837093696 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
[W::hts_idx_load3] The index file is older than the data file: Sig_18_Blood.recalibrated.bam.bai
I0605 14:00:29.783485 140527781259072 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
I0605 14:00:29.792789 140527781259072 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 14:00:29.783480 139659837093696 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
I0605 14:00:29.792791 139659837093696 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 14:00:29.766257 140161010882368 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 14:00:29.786091 140161010882368 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
I0605 14:00:29.795188 140161010882368 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 14:00:29.767176 140588518889280 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 14:00:29.786105 140588518889280 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
I0605 14:00:29.795308 140588518889280 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 14:00:30.060821 139659837093696 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']
I0605 14:00:30.061044 140161010882368 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']
I0605 14:00:30.067281 140588518889280 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']
I0605 14:00:30.165207 140527781259072 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']
I0605 14:00:30.237338 139659837093696 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0605 14:00:30.243531 140161010882368 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0605 14:00:30.330608 140588518889280 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0605 14:00:30.349848 140527781259072 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0605 14:00:30.480108 139659837093696 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
I0605 14:00:30.528828 139659837093696 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
I0605 14:00:30.491433 140161010882368 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
I0605 14:00:30.535688 140161010882368 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 14:00:30.583157 140527781259072 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
I0605 14:00:30.627903 140527781259072 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
I0605 14:00:30.671272 140527781259072 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 14:00:30.671892 140527781259072 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0605 14:00:30.672291 140527781259072 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0605 14:00:30.672346 140527781259072 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0605 14:00:30.674486 140527781259072 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0605 14:00:30.572268 139659837093696 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 14:00:30.572873 139659837093696 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0605 14:00:30.573348 139659837093696 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0605 14:00:30.573406 139659837093696 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0605 14:00:30.575558 139659837093696 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
I0605 14:00:30.580303 140161010882368 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 14:00:30.580925 140161010882368 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0605 14:00:30.581489 140161010882368 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0605 14:00:30.581555 140161010882368 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0605 14:00:30.583952 140161010882368 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0605 14:00:30.578783 140588518889280 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
I0605 14:00:30.620695 140588518889280 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
I0605 14:00:30.664135 140588518889280 genomics_reader.py:222] Reading Sig_18_Blood.recalibrated.bam with NativeSamReader
I0605 14:00:30.664764 140588518889280 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0605 14:00:30.665226 140588518889280 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0605 14:00:30.665301 140588518889280 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0605 14:00:30.668163 140588518889280 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0605 14:00:32.077888 140527781259072 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0605 14:00:32.078063 140527781259072 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0605 14:00:32.078460 140527781259072 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0605 14:00:32.078900 140527781259072 make_examples_core.py:301] Task 1/4: Found 2 candidate variants
I0605 14:00:32.078932 140527781259072 make_examples_core.py:301] Task 1/4: Created 2 examples
I0605 14:00:32.132947 139659837093696 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0605 14:00:32.133111 139659837093696 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0605 14:00:32.133510 139659837093696 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0605 14:00:32.133896 139659837093696 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0605 14:00:32.133925 139659837093696 make_examples_core.py:301] Task 3/4: Created 4 examples
I0605 14:00:32.572534 140161010882368 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0605 14:00:32.572865 140161010882368 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0605 14:00:32.573451 140161010882368 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0605 14:00:32.574138 140161010882368 make_examples_core.py:301] Task 2/4: Found 4 candidate variants
I0605 14:00:32.574188 140161010882368 make_examples_core.py:301] Task 2/4: Created 4 examples
I0605 14:00:32.741029 140588518889280 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0605 14:00:32.741398 140588518889280 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0605 14:00:32.742277 140588518889280 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0605 14:00:32.742942 140588518889280 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0605 14:00:32.742987 140588518889280 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m5.241s
user 0m29.580s
sys 0m39.315s
***** 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(
I0605 14:00:34.955466 139762067040064 call_variants.py:563] Total 1 writing processes started.
I0605 14:00:34.956888 139762067040064 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].
I0605 14:00:34.956957 139762067040064 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0605 14:00:34.957226 139762067040064 call_variants.py:592] Use saved model: True
I0605 14:00:39.166960 139762067040064 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].
I0605 14:00:39.167131 139762067040064 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].
I0605 14:00:39.922334 139762067040064 call_variants.py:716] Predicted 19 examples in 1 batches [3.343 sec per 100].
I0605 14:00:40.045043 139762067040064 call_variants.py:779] Complete: call_variants.
real 0m7.868s
user 0m13.698s
sys 0m14.990s
***** 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"
I0605 14:00:42.652739 140351483397952 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
2026-06-05 14:00:42.656475: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-05 14:00:42.656623: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 19
I0605 14:00:42.657681 140351483397952 postprocess_variants.py:1313] CVO sorting took 7.511774698893229e-05 minutes
I0605 14:00:42.657828 140351483397952 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0605 14:00:42.657856 140351483397952 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0605 14:00:42.677478 140351483397952 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: Sig_18_Blood
I0605 14:00:42.683384 140351483397952 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 5.596478780110677e-05 minutes
I0605 14:00:42.773383 140351483397952 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.001497972011566162 minutes.
real 0m2.016s
user 0m4.986s
sys 0m9.615s
***** 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"
I0605 14:00:44.624897 140141298087744 genomics_reader.py:222] Reading germline_control_2.dv_rescue.vcf.gz with NativeVcfReader
real 0m1.900s
user 0m5.158s
sys 0m9.310s