Genome Analysis Toolkit

WKaiser · November 19, 2020 10:23

i am writing a workflow for variant discovery, when i use CNNScoreVariants i get the error: AttributeError: 'str' object has no attribute 'decode'. I attached the error log below

I test the workflow by using it on the mitochondrial genome and on Chromosome 8 (hg19). I tried samtools and gatk Haplotypecaller for Variant calling, vcfs from both result in the same error.

a) gatk 4.1.9.0

To write the workflow i use snakemake with conda:

conda version: 4.9.2

snakemake-minimal: 5.28.0

python: 3.8.3

java: openjdk: 11.0.9.1 2020-11-04

i built the conda gatk environment as described in the gatk-guide here:

https://gatk.broadinstitute.org/hc/en-us/articles/360035889851--How-to-Install-and-use-Conda-for-GATK4

gatkpythonpackages in the conda environment are version 0.1

i also activate gatk 4.1.9.0 with the PATH command:

PATH=$PATH:/home/wk/daten1/tools/gatk-4.1.9.0/

b) gatk CNNScoreVariants -V data/variance_call/all_samtools.vcf -R chrom/chrM.fa -O data/variance_call_cnnscored/all_samtools_cnnscored.vcf

command with Java options under the "Running" entry in the log.

c) the entire error log is below.

If needed i will provide additional information as quickly as possible.

My thanks in advance for clues on how to solve this.

Error log:

17:58:22.221 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/wk/daten1/praktikum/tools/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Nov 16, 2020 5:58:22 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
17:58:22.362 INFO CNNScoreVariants - ------------------------------------------------------------
17:58:22.362 INFO CNNScoreVariants - The Genome Analysis Toolkit (GATK) v4.1.9.0
17:58:22.362 INFO CNNScoreVariants - For support and documentation go to https://software.broadinstitute.org/gatk/
17:58:22.362 INFO CNNScoreVariants - Executing as wk@wk on Linux v5.4.0-53-generic amd64
17:58:22.362 INFO CNNScoreVariants - Java runtime: OpenJDK 64-Bit Server VM v11.0.9.1+1-Ubuntu-0ubuntu1.20.04
17:58:22.363 INFO CNNScoreVariants - Start Date/Time: 16. November 2020 um 17:58:22 MEZ
17:58:22.363 INFO CNNScoreVariants - ------------------------------------------------------------
17:58:22.363 INFO CNNScoreVariants - ------------------------------------------------------------
17:58:22.363 INFO CNNScoreVariants - HTSJDK Version: 2.23.0
17:58:22.363 INFO CNNScoreVariants - Picard Version: 2.23.3
17:58:22.363 INFO CNNScoreVariants - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:58:22.363 INFO CNNScoreVariants - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:58:22.363 INFO CNNScoreVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:58:22.363 INFO CNNScoreVariants - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:58:22.363 INFO CNNScoreVariants - Deflater: IntelDeflater
17:58:22.363 INFO CNNScoreVariants - Inflater: IntelInflater
17:58:22.364 INFO CNNScoreVariants - GCS max retries/reopens: 20
17:58:22.364 INFO CNNScoreVariants - Requester pays: disabled
17:58:22.364 INFO CNNScoreVariants - Initializing engine
17:58:22.474 INFO FeatureManager - Using codec VCFCodec to read file file:///home/wk/daten1/praktikum/Variant_calling_uebung/data/variance_call/all_samtools.vcf
17:58:22.493 INFO CNNScoreVariants - Done initializing engine
17:58:22.494 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/wk/daten1/praktikum/tools/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar!/com/intel/gkl/native/libgkl_utils.so
17:58:24.607 INFO CNNScoreVariants - Using key:CNN_1D for CNN architecture:/tmp/1d_cnn_mix_train_full_bn.5588241428780893532.json and weights:/tmp/1d_cnn_mix_train_full_bn.12745529145956847191.hd5
17:58:24.701 INFO CNNScoreVariants - Done scoring variants with CNN.
17:58:24.701 INFO CNNScoreVariants - Shutting down engine
[16. November 2020 um 17:58:24 MEZ] org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=169869312
org.broadinstitute.hellbender.utils.python.PythonScriptExecutorException: A nack was received from the Python process (most likely caused by a raised exception caused by): nkm received

: Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/wk/miniconda3/envs/gatk/lib/python3.6/site-packages/vqsr_cnn/vqsr_cnn/models.py", line 26, in start_session_get_args_and_model return args_and_model_from_semantics(semantics_json, weights_hd5, tensor_type)
File "/home/wk/miniconda3/envs/gatk/lib/python3.6/site-packages/vqsr_cnn/vqsr_cnn/models.py", line 33, in args_and_model_from_semantics model = set_args_and_get_model_from_semantics(args, semantics_json, weights_hd5)
File "/home/wk/miniconda3/envs/gatk/lib/python3.6/site-packages/vqsr_cnn/vqsr_cnn/models.py", line 90, in set_args_and_get_model_from_semantics model = load_model(weights_hd5, custom_objects=get_metric_dict(args.labels))
File "/home/wk/miniconda3/envs/gatk/lib/python3.6/site-packages/keras/engine/saving.py", line 419, in load_model model = _deserialize_model(f, custom_objects, compile)
File "/home/wk/miniconda3/envs/gatk/lib/python3.6/site-packages/keras/engine/saving.py", line 224, in _deserialize_model model_config = json.loads(model_config.decode('utf-8'))

AttributeError: 'str' object has no attribute 'decode'

at org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor.waitForAck(StreamingPythonScriptExecutor.java:222)
at org.broadinstitute.hellbender.utils.python.StreamingPythonScriptExecutor.sendSynchronousCommand(StreamingPythonScriptExecutor.java:183)
at org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants.initializePythonArgsAndModel(CNNScoreVariants.java:561)
at org.broadinstitute.hellbender.tools.walkers.vqsr.CNNScoreVariants.onTraversalStart(CNNScoreVariants.java:321)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1047)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
Using GATK jar /home/wk/daten1/praktikum/tools/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar

Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/wk/daten1/praktikum/tools/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar CNNScoreVariants -V data/variance_call/all_samtools.vcf -R chrom/chrM.fa -O data/variance_call_cnnscored/all_samtools_cnnscored.vcf

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CNNScoreVariants error: AttributeError: 'str' object has no attribute 'decode'

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