warnings in the output of DeepVariant command #920
Description
Dear DeepVariant team,
I run DeepVariant command based on DeepVariant quick start. I saw some warnings and I am not sure about these warnings.
Could you guild me about this warnings?
Best regards,
Alireza.
(base) bear@bear:~/alireza/deepvariant$ sudo docker run
-v "${INPUT_DIR}":"/input"
-v "${OUTPUT_DIR}":"/output"
google/deepvariant:"${BIN_VERSION}"
/opt/deepvariant/bin/run_deepvariant
--model_type=WGS
--vcf_stats_report=true
--ref=/input/ucsc.hg19.chr20.unittest.fasta
--reads=/input/NA12878_S1.chr20.10_10p1mb.bam
--regions "chr20:10,000,000-10,010,000"
--output_vcf=/output/output.vcf.gz
--output_gvcf=/output/output.g.vcf.gz
--intermediate_results_dir /output/intermediate_results_dir
--num_shards=1
[sudo] password for bear:
2024-12-28 16:10:45.473731: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 AVX512F AVX512_VNNI AVX512_BF16 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
2024-12-28 16:10:45.540276: I tensorflow/core/util/port.cc:104] oneDNN custom operations are on. You may see slightly different numerical results due to floating-point round-off errors from different computation orders. To turn them off, set the environment variable TF_ENABLE_ONEDNN_OPTS=0.
2024-12-28 16:10:45.542603: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2024-12-28 16:10:45.542613: I tensorflow/compiler/xla/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
2024-12-28 16:10:46.010168: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory
2024-12-28 16:10:46.010228: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory
2024-12-28 16:10:46.010233: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.
2024-12-28 16:10:46.699474: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory
2024-12-28 16:10:46.699493: W tensorflow/compiler/xla/stream_executor/cuda/cuda_driver.cc:265] failed call to cuInit: UNKNOWN ERROR (303)
2024-12-28 16:10:46.699507: I tensorflow/compiler/xla/stream_executor/cuda/cuda_diagnostics.cc:163] no NVIDIA GPU device is present: /dev/nvidia0 does not exist
I1228 16:10:46.699570 127594862972928 run_deepvariant.py:643] Creating a directory for intermediate results in /output/intermediate_results_dir
***** Intermediate results will be written to /output/intermediate_results_dir in docker. ****
***** Running the command:*****
time seq 0 0 | parallel -q --halt 2 --line-buffer /opt/deepvariant/bin/make_examples --mode calling --ref "/input/ucsc.hg19.chr20.unittest.fasta" --reads "/input/NA12878_S1.chr20.10_10p1mb.bam" --examples "/output/intermediate_results_dir/make_examples.tfrecord@1.gz" --checkpoint "/opt/models/wgs" --call_small_model_examples --gvcf "/output/intermediate_results_dir/gvcf.tfrecord@1.gz" --regions "chr20:10,000,000-10,010,000" --small_model_indel_gq_threshold "30" --small_model_snp_gq_threshold "25" --small_model_vaf_context_window_size "51" --trained_small_model_path "/opt/smallmodels/wgs" --task {}
I1228 16:10:46.699922 127594862972928 run_deepvariant.py:847] env = {'HOSTNAME': '11a3b8cb1891', 'PYTHON_VERSION': '3.10', 'DV_GPU_BUILD': '0', 'PWD': '/opt/deepvariant', 'TF_ENABLE_ONEDNN_OPTS': '1', 'HOME': '/root', 'SHLVL': '1', 'PATH': '/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/conda/bin:/opt/conda/envs/bio/bin:/opt/deepvariant/bin', 'VERSION': '1.8.0', '_': '/usr/bin/python3', 'LC_CTYPE': 'C.UTF-8', 'TPU_ML_PLATFORM': 'Tensorflow', 'TF2_BEHAVIOR': '1', 'TF_CPP_MIN_LOG_LEVEL': '1'}
2024-12-28 16:10:47.252359: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2024-12-28 16:10:47.548985: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory
2024-12-28 16:10:47.549017: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory
2024-12-28 16:10:47.549020: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.
/usr/local/lib/python3.10/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: tensorflow/addons#2807
warnings.warn(
2024-12-28 16:10:48.250534: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory
2024-12-28 16:10:48.250546: W tensorflow/compiler/xla/stream_executor/cuda/cuda_driver.cc:265] failed call to cuInit: UNKNOWN ERROR (303)
I1228 16:10:48.250900 136107432939520 genomics_reader.py:223] Reading /input/NA12878_S1.chr20.10_10p1mb.bam with NativeSamReader
I1228 16:10:48.251638 136107432939520 dv_utils.py:325] From /opt/models/wgs/example_info.json: Shape of input examples: [100, 221, 7], Channels of input examples: [1, 2, 3, 4, 5, 6, 19].
I1228 16:10:48.254233 136107432939520 make_examples_core.py:322] Preparing inputs
I1228 16:10:48.254390 136107432939520 genomics_reader.py:223] Reading /input/NA12878_S1.chr20.10_10p1mb.bam with NativeSamReader
I1228 16:10:48.254612 136107432939520 make_examples_core.py:322] Common contigs are ['chr20']
I1228 16:10:48.493595 136107432939520 make_examples_core.py:322] 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
I1228 16:10:48.495226 136107432939520 genomics_reader.py:223] Reading /input/NA12878_S1.chr20.10_10p1mb.bam with NativeSamReader
I1228 16:10:48.560587 136107432939520 genomics_reader.py:223] Reading /input/NA12878_S1.chr20.10_10p1mb.bam with NativeSamReader
I1228 16:10:48.560690 136107432939520 make_examples_core.py:322] Writing gvcf records to /output/intermediate_results_dir/gvcf.tfrecord-00000-of-00001.gz
I1228 16:10:48.561406 136107432939520 make_examples_core.py:322] Writing examples to /output/intermediate_results_dir/make_examples.tfrecord-00000-of-00001.gz
I1228 16:10:48.561437 136107432939520 make_examples_core.py:322] Overhead for preparing inputs: 0 seconds
I1228 16:10:48.656072 136107432939520 make_examples_core.py:322] 6 candidates (1 examples) [0.09s elapsed]
I1228 16:10:49.193665 136107432939520 make_examples_core.py:322] Writing example info to /output/intermediate_results_dir/make_examples.tfrecord-00000-of-00001.gz.example_info.json
I1228 16:10:49.193746 136107432939520 make_examples_core.py:3175] example_shape = [100, 221, 7]
I1228 16:10:49.193766 136107432939520 make_examples_core.py:3176] example_channels = [1, 2, 3, 4, 5, 6, 19]
I1228 16:10:49.193965 136107432939520 make_examples_core.py:322] Found 78 candidate variants
I1228 16:10:49.193990 136107432939520 make_examples_core.py:322] Created 22 examples
I1228 16:10:49.194005 136107432939520 make_examples_core.py:322] Created 0 small model examples
I1228 16:10:49.194018 136107432939520 make_examples_core.py:322] Small Model called 62 candidates
real 0m2.822s
user 0m4.502s
sys 0m2.088s
***** Running the command:*****
time /opt/deepvariant/bin/call_variants --outfile "/output/intermediate_results_dir/call_variants_output.tfrecord.gz" --examples "/output/intermediate_results_dir/make_examples.tfrecord@1.gz" --checkpoint "/opt/models/wgs"
2024-12-28 16:10:49.816191: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2024-12-28 16:10:50.194286: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory
2024-12-28 16:10:50.194322: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory
2024-12-28 16:10:50.194325: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.
/usr/local/lib/python3.10/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: tensorflow/addons#2807
warnings.warn(
2024-12-28 16:10:51.056151: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory
2024-12-28 16:10:51.056166: W tensorflow/compiler/xla/stream_executor/cuda/cuda_driver.cc:265] failed call to cuInit: UNKNOWN ERROR (303)
I1228 16:10:51.056234 139675775700992 call_variants.py:918] call_variants: env = {'HOSTNAME': '11a3b8cb1891', 'PYTHON_VERSION': '3.10', 'TF_CPP_MIN_LOG_LEVEL': '1', 'DV_GPU_BUILD': '0', 'PWD': '/opt/deepvariant', 'TF_ENABLE_ONEDNN_OPTS': '1', '_': '/usr/bin/python3', 'HOME': '/root', 'TPU_ML_PLATFORM': 'Tensorflow', 'SHLVL': '3', 'LC_CTYPE': 'C.UTF-8', 'PATH': '/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/conda/bin:/opt/conda/envs/bio/bin:/opt/deepvariant/bin', 'TF2_BEHAVIOR': '1', 'VERSION': '1.8.0', 'PYTHONPATH': '/tmp/Bazel.runfiles_lv2eh_r1/runfiles:/tmp/Bazel.runfiles_lv2eh_r1/runfiles/com_google_protobuf/python:/tmp/Bazel.runfiles_lv2eh_r1/runfiles/absl_py:/tmp/Bazel.runfiles_lv2eh_r1/runfiles/bazel_tools:/tmp/Bazel.runfiles_lv2eh_r1/runfiles/com_google_deepvariant:/tmp/Bazel.runfiles_lv2eh_r1/runfiles/com_google_protobuf:/tmp/Bazel.runfiles_lv2eh_r1/runfiles/six_archive', 'RUNFILES_DIR': '/tmp/Bazel.runfiles_lv2eh_r1/runfiles'}
I1228 16:10:51.064217 139675775700992 call_variants.py:785] Total 1 writing processes started.
I1228 16:10:51.065089 139675775700992 call_variants.py:796] Use saved model: True
I1228 16:10:51.065470 139675775700992 dv_utils.py:325] From /output/intermediate_results_dir/make_examples.tfrecord-00000-of-00001.gz.example_info.json: Shape of input examples: [100, 221, 7], Channels of input examples: [1, 2, 3, 4, 5, 6, 19].
I1228 16:10:53.779392 139675775700992 dv_utils.py:325] From /opt/models/wgs/example_info.json: Shape of input examples: [100, 221, 7], Channels of input examples: [1, 2, 3, 4, 5, 6, 19].
I1228 16:10:53.779490 139675775700992 call_variants.py:814] example_shape: [100, 221, 7]
I1228 16:10:54.350414 139675775700992 call_variants.py:891] Predicted 22 examples in 1 batches [1.253 sec per 100].
I1228 16:10:54.396512 139675775700992 call_variants.py:967] Complete: call_variants.
real 0m5.543s
user 0m7.714s
sys 0m2.230s
***** Running the command:*****
time /opt/deepvariant/bin/postprocess_variants --ref "/input/ucsc.hg19.chr20.unittest.fasta" --infile "/output/intermediate_results_dir/call_variants_output.tfrecord.gz" --outfile "/output/output.vcf.gz" --cpus "1" --small_model_cvo_records "/output/intermediate_results_dir/make_examples_call_variant_outputs.tfrecord@1.gz" --gvcf_outfile "/output/output.g.vcf.gz" --nonvariant_site_tfrecord_path "/output/intermediate_results_dir/gvcf.tfrecord@1.gz" --regions "chr20:10,000,000-10,010,000"
2024-12-28 16:10:55.368256: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2024-12-28 16:10:55.743046: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory
2024-12-28 16:10:55.743091: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory
2024-12-28 16:10:55.743095: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.
2024-12-28 16:10:56.406978: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory
2024-12-28 16:10:56.406993: W tensorflow/compiler/xla/stream_executor/cuda/cuda_driver.cc:265] failed call to cuInit: UNKNOWN ERROR (303)
I1228 16:10:56.407692 137050720653312 postprocess_variants.py:1445] Using sample name from call_variants output. Sample name: NA12878
I1228 16:10:56.408358 137050720653312 postprocess_variants.py:1318] CVO sorting took 4.8836072285970054e-06 minutes
I1228 16:10:56.408421 137050720653312 postprocess_variants.py:1322] Transforming call_variants_output to variants.
I1228 16:10:56.408440 137050720653312 postprocess_variants.py:1330] Processed 84 variants.
I1228 16:10:56.408485 137050720653312 postprocess_variants.py:1533] Processing variants (and writing to temporary files) took 7.092952728271484e-06 minutes
I1228 16:10:56.665696 137050720653312 postprocess_variants.py:1568] VCF and gVCF creation took 0.004286126295725504 minutes.
I1228 16:10:56.676080 137050720653312 postprocess_variants.py:1723] Indexing VCF and gVCF took 0.00017061233520507813 minutes.
real 0m1.890s
user 0m3.615s
sys 0m1.947s
***** Running the command:*****
time /opt/deepvariant/bin/vcf_stats_report --input_vcf "/output/output.vcf.gz" --outfile_base "/output/output"
2024-12-28 16:10:57.196252: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory
2024-12-28 16:10:57.627780: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer.so.7'; dlerror: libnvinfer.so.7: cannot open shared object file: No such file or directory
2024-12-28 16:10:57.627816: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libnvinfer_plugin.so.7'; dlerror: libnvinfer_plugin.so.7: cannot open shared object file: No such file or directory
2024-12-28 16:10:57.627819: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Cannot dlopen some TensorRT libraries. If you would like to use Nvidia GPU with TensorRT, please make sure the missing libraries mentioned above are installed properly.
2024-12-28 16:10:58.318505: W tensorflow/compiler/xla/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcuda.so.1'; dlerror: libcuda.so.1: cannot open shared object file: No such file or directory
2024-12-28 16:10:58.318520: W tensorflow/compiler/xla/stream_executor/cuda/cuda_driver.cc:265] failed call to cuInit: UNKNOWN ERROR (303)
I1228 16:10:58.318864 130550458163200 genomics_reader.py:223] Reading /output/output.vcf.gz with NativeVcfReader
real 0m1.784s
user 0m3.572s
sys 0m1.909s