***** 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
I0605 20:52:38.181994 139768934623040 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 20:52:38.195641 139768934623040 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
I0605 20:52:38.204344 139768934623040 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
I0605 20:52:38.182107 139633500473152 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 20:52:38.196401 139633500473152 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
I0605 20:52:38.205132 139633500473152 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
I0605 20:52:38.181070 140393334642496 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 20:52:38.195589 140393334642496 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
I0605 20:52:38.204097 140393334642496 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
I0605 20:52:38.197916 140327267952448 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 20:52:38.208510 140327267952448 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
I0605 20:52:38.216997 140327267952448 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 20:52:38.483932 139768934623040 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 20:52:38.480191 139633500473152 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 20:52:38.479458 140393334642496 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 20:52:38.497061 140327267952448 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 20:52:38.645763 139768934623040 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0605 20:52:38.638910 139633500473152 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0605 20:52:38.634497 140393334642496 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0605 20:52:38.658457 140327267952448 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0605 20:52:38.884412 139768934623040 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
I0605 20:52:38.923158 139768934623040 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
I0605 20:52:38.966475 139768934623040 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 20:52:38.967179 139768934623040 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0605 20:52:38.967635 139768934623040 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0605 20:52:38.967682 139768934623040 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 0 seconds
I0605 20:52:38.970072 139768934623040 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0605 20:52:38.870741 139633500473152 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
I0605 20:52:38.912355 139633500473152 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
I0605 20:52:38.954905 139633500473152 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 20:52:38.955616 139633500473152 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0605 20:52:38.956123 139633500473152 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0605 20:52:38.956172 139633500473152 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0605 20:52:38.958616 139633500473152 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0605 20:52:38.863095 140393334642496 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
I0605 20:52:38.902629 140393334642496 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
I0605 20:52:38.945196 140393334642496 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 20:52:38.945772 140393334642496 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0605 20:52:38.946188 140393334642496 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0605 20:52:38.946233 140393334642496 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 0 seconds
I0605 20:52:38.948495 140393334642496 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0605 20:52:38.903779 140327267952448 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
I0605 20:52:38.942457 140327267952448 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
I0605 20:52:38.985317 140327267952448 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0605 20:52:38.985915 140327267952448 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0605 20:52:38.986340 140327267952448 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0605 20:52:38.986390 140327267952448 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 0 seconds
I0605 20:52:38.989365 140327267952448 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0605 20:52:40.450607 139768934623040 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0605 20:52:40.450953 139768934623040 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0605 20:52:40.451730 139768934623040 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0605 20:52:40.452385 139768934623040 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0605 20:52:40.452429 139768934623040 make_examples_core.py:301] Task 1/4: Created 1 examples
I0605 20:52:40.441985 140393334642496 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0605 20:52:40.442306 140393334642496 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0605 20:52:40.442771 140393334642496 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0605 20:52:40.443454 140393334642496 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0605 20:52:40.443502 140393334642496 make_examples_core.py:301] Task 3/4: Created 4 examples
I0605 20:52:40.838564 139633500473152 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0605 20:52:40.838714 139633500473152 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0605 20:52:40.839090 139633500473152 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0605 20:52:40.839442 139633500473152 make_examples_core.py:301] Task 2/4: Found 6 candidate variants
I0605 20:52:40.839471 139633500473152 make_examples_core.py:301] Task 2/4: Created 6 examples
I0605 20:52:41.738763 140327267952448 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0605 20:52:41.739239 140327267952448 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0605 20:52:41.740060 140327267952448 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0605 20:52:41.740743 140327267952448 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0605 20:52:41.740795 140327267952448 make_examples_core.py:301] Task 0/4: Created 9 examples
real 0m5.667s
user 0m23.322s
sys 0m38.105s
***** 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 20:52:43.864237 140164613322560 call_variants.py:563] Total 1 writing processes started.
I0605 20:52:43.865582 140164613322560 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 20:52:43.865639 140164613322560 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0605 20:52:43.865850 140164613322560 call_variants.py:592] Use saved model: True
I0605 20:52:47.573894 140164613322560 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 20:52:47.574049 140164613322560 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 20:52:48.208106 140164613322560 call_variants.py:716] Predicted 20 examples in 1 batches [2.644 sec per 100].
I0605 20:52:48.278540 140164613322560 call_variants.py:779] Complete: call_variants.
real 0m6.846s
user 0m10.507s
sys 0m13.043s
***** 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"
I0605 20:52:50.552276 139683066898240 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-06-05 20:52:50.555822: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-06-05 20:52:50.555952: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 20
I0605 20:52:50.556992 139683066898240 postprocess_variants.py:1313] CVO sorting took 7.252295811971029e-05 minutes
I0605 20:52:50.557109 139683066898240 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0605 20:52:50.557136 139683066898240 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0605 20:52:50.574029 139683066898240 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0605 20:52:50.579395 139683066898240 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 4.8371156056722003e-05 minutes
I0605 20:52:50.677251 139683066898240 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.001629324754079183 minutes.
real 0m1.964s
user 0m4.676s
sys 0m11.437s
***** 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"
I0605 20:52:52.476939 140717084755776 genomics_reader.py:222] Reading germline_control_1.dv_rescue.vcf.gz with NativeVcfReader
real 0m1.874s
user 0m4.593s
sys 0m11.409s