.command.out - Workdir - DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE (germline_control_1;germline_rescue_targets)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1f/22468d9cdddf5cbd560fbf507e81db/.command.out
Size: 13.1 KB
Task: DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:DV_RESCUE (germline_control_1;germline_rescue_targets)
Attempt
Content

***** 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 {}

I0527 23:56:29.500827 139959680898880 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 23:56:29.512913 139959680898880 make_examples_core.py:301] Task 1/4: Preparing inputs
I0527 23:56:29.522612 139959680898880 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 23:56:29.490796 139722462771008 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 23:56:29.503222 139722462771008 make_examples_core.py:301] Task 0/4: Preparing inputs
I0527 23:56:29.513057 139722462771008 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 23:56:29.385275 139858142820160 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 23:56:29.398760 139858142820160 make_examples_core.py:301] Task 2/4: Preparing inputs
I0527 23:56:29.408832 139858142820160 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 23:56:29.758303 139641859192640 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 23:56:29.776377 139641859192640 make_examples_core.py:301] Task 3/4: Preparing inputs
I0527 23:56:29.790920 139641859192640 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 23:56:29.710605 139858142820160 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']
I0527 23:56:29.824493 139959680898880 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']
I0527 23:56:29.854930 139722462771008 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']
I0527 23:56:29.974298 139858142820160 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 23:56:30.299365 139641859192640 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']
I0527 23:56:30.102207 139959680898880 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 23:56:30.142132 139722462771008 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 23:56:30.303256 139858142820160 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
I0527 23:56:30.337752 139858142820160 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 23:56:30.473255 139959680898880 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
I0527 23:56:30.511872 139959680898880 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 23:56:30.567510 139959680898880 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 23:56:30.568369 139959680898880 make_examples_core.py:301] Task 1/4: Writing gvcf records to tmp/gvcf.tfrecord-00001-of-00004.gz
I0527 23:56:30.568953 139959680898880 make_examples_core.py:301] Task 1/4: Writing examples to tmp/make_examples.tfrecord-00001-of-00004.gz
I0527 23:56:30.569045 139959680898880 make_examples_core.py:301] Task 1/4: Overhead for preparing inputs: 1 seconds
I0527 23:56:30.571664 139959680898880 make_examples_core.py:301] Task 1/4: 0 candidates (0 examples) [0.00s elapsed]
I0527 23:56:30.459374 139722462771008 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
I0527 23:56:30.493395 139722462771008 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 23:56:30.544349 139722462771008 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 23:56:30.545147 139722462771008 make_examples_core.py:301] Task 0/4: Writing gvcf records to tmp/gvcf.tfrecord-00000-of-00004.gz
I0527 23:56:30.545730 139722462771008 make_examples_core.py:301] Task 0/4: Writing examples to tmp/make_examples.tfrecord-00000-of-00004.gz
I0527 23:56:30.545802 139722462771008 make_examples_core.py:301] Task 0/4: Overhead for preparing inputs: 1 seconds
I0527 23:56:30.549208 139722462771008 make_examples_core.py:301] Task 0/4: 0 candidates (0 examples) [0.00s elapsed]
I0527 23:56:30.386820 139858142820160 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 23:56:30.387597 139858142820160 make_examples_core.py:301] Task 2/4: Writing gvcf records to tmp/gvcf.tfrecord-00002-of-00004.gz
I0527 23:56:30.388142 139858142820160 make_examples_core.py:301] Task 2/4: Writing examples to tmp/make_examples.tfrecord-00002-of-00004.gz
I0527 23:56:30.388207 139858142820160 make_examples_core.py:301] Task 2/4: Overhead for preparing inputs: 0 seconds
I0527 23:56:30.391566 139858142820160 make_examples_core.py:301] Task 2/4: 0 candidates (0 examples) [0.00s elapsed]
I0527 23:56:30.736206 139641859192640 genomics_reader.py:222] Reading germline_rescue_targets.bed with NativeBedReader
I0527 23:56:31.203898 139641859192640 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
I0527 23:56:31.243867 139641859192640 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 23:56:31.314907 139641859192640 genomics_reader.py:222] Reading HCC1395_BL.recalibrated.bam with NativeSamReader
I0527 23:56:31.315975 139641859192640 make_examples_core.py:301] Task 3/4: Writing gvcf records to tmp/gvcf.tfrecord-00003-of-00004.gz
I0527 23:56:31.316747 139641859192640 make_examples_core.py:301] Task 3/4: Writing examples to tmp/make_examples.tfrecord-00003-of-00004.gz
I0527 23:56:31.316849 139641859192640 make_examples_core.py:301] Task 3/4: Overhead for preparing inputs: 1 seconds
I0527 23:56:31.320680 139641859192640 make_examples_core.py:301] Task 3/4: 0 candidates (0 examples) [0.00s elapsed]
I0527 23:56:32.524039 139858142820160 make_examples_core.py:301] Task 2/4: Writing example info to tmp/make_examples.tfrecord-00002-of-00004.gz.example_info.json
I0527 23:56:32.524280 139858142820160 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 23:56:32.524808 139858142820160 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 23:56:32.525295 139858142820160 make_examples_core.py:301] Task 2/4: Found 6 candidate variants
I0527 23:56:32.525333 139858142820160 make_examples_core.py:301] Task 2/4: Created 6 examples
I0527 23:56:33.177391 139641859192640 make_examples_core.py:301] Task 3/4: Writing example info to tmp/make_examples.tfrecord-00003-of-00004.gz.example_info.json
I0527 23:56:33.177618 139641859192640 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 23:56:33.178137 139641859192640 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 23:56:33.178620 139641859192640 make_examples_core.py:301] Task 3/4: Found 4 candidate variants
I0527 23:56:33.178653 139641859192640 make_examples_core.py:301] Task 3/4: Created 4 examples
I0527 23:56:32.993175 139959680898880 make_examples_core.py:301] Task 1/4: Writing example info to tmp/make_examples.tfrecord-00001-of-00004.gz.example_info.json
I0527 23:56:32.993456 139959680898880 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 23:56:32.994031 139959680898880 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 23:56:32.994640 139959680898880 make_examples_core.py:301] Task 1/4: Found 1 candidate variants
I0527 23:56:32.994708 139959680898880 make_examples_core.py:301] Task 1/4: Created 1 examples
I0527 23:56:33.870887 139722462771008 make_examples_core.py:301] Task 0/4: Writing example info to tmp/make_examples.tfrecord-00000-of-00004.gz.example_info.json
I0527 23:56:33.871219 139722462771008 make_examples_core.py:2958] example_shape = [100, 221, 7]
I0527 23:56:33.872242 139722462771008 make_examples_core.py:2959] example_channels = [1, 2, 3, 4, 5, 6, 19]
I0527 23:56:33.872921 139722462771008 make_examples_core.py:301] Task 0/4: Found 4 candidate variants
I0527 23:56:33.872974 139722462771008 make_examples_core.py:301] Task 0/4: Created 9 examples

real	0m7.418s
user	0m27.952s
sys	0m22.415s

***** 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(
I0527 23:56:36.672416 140710046668608 call_variants.py:563] Total 1 writing processes started.
I0527 23:56:36.674335 140710046668608 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].
I0527 23:56:36.674433 140710046668608 call_variants.py:588] Shape of input examples: [100, 221, 7]
I0527 23:56:36.674695 140710046668608 call_variants.py:592] Use saved model: True
I0527 23:56:41.199014 140710046668608 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].
I0527 23:56:41.199241 140710046668608 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].
I0527 23:56:42.527982 140710046668608 call_variants.py:716] Predicted 20 examples in 1 batches [5.952 sec per 100].
I0527 23:56:42.607640 140710046668608 call_variants.py:779] Complete: call_variants.

real	0m8.976s
user	0m11.173s
sys	0m11.510s

***** 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"

I0527 23:56:45.400377 140553507071808 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
2026-05-27 23:56:45.404426: I deepvariant/postprocess_variants.cc:94] Read from: tmp/call_variants_output-00000-of-00001.tfrecord.gz
2026-05-27 23:56:45.404573: I deepvariant/postprocess_variants.cc:109] Total #entries in single_site_calls = 20
I0527 23:56:45.405599 140553507071808 postprocess_variants.py:1313] CVO sorting took 7.744232813517253e-05 minutes
I0527 23:56:45.405812 140553507071808 postprocess_variants.py:1316] Transforming call_variants_output to variants.
I0527 23:56:45.405843 140553507071808 postprocess_variants.py:1318] Using 4 CPUs for parallelization of variant transformation.
I0527 23:56:45.422418 140553507071808 postprocess_variants.py:1211] Using sample name from call_variants output. Sample name: HCC1395_BL
I0527 23:56:45.428689 140553507071808 postprocess_variants.py:1386] Processing variants (and writing to temporary file) took 4.457235336303711e-05 minutes
I0527 23:56:45.569334 140553507071808 postprocess_variants.py:1407] Finished writing VCF and gVCF in 0.0023410956064860025 minutes.

real	0m2.443s
user	0m4.346s
sys	0m10.644s

***** 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"

I0527 23:56:47.805894 140005048309568 genomics_reader.py:222] Reading germline_control_1.dv_rescue.vcf.gz with NativeVcfReader

real	0m2.278s
user	0m3.979s
sys	0m10.843s