UnifiedGenotyper error on Solid data

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Mariano Avino

• February 20, 2020 18:41
• Edited

Can you please provide
a) GATK version used: UnifiedGenotyper (

toolshed.g2.bx.psu.edu/repos/devteam/unified_genotyper/gatk_unified_genotyper/0.0.6

)
b) Exact GATK commands use:

python /cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/unified_genotyper/66dd4d4c1743/unified_genotyper/gatk_wrapper.py --max_jvm_heap_fraction "1" --stdout "/galaxy-repl/main/files/037/873/dataset_37873918.dat" -d "-I" "/galaxy-repl/main/files/037/843/dataset_37843952.dat" "bam" "gatk_input_0" -d "" "/galaxy-repl/main/files/_metadata_files/002/879/metadata_2879220.dat" "bam_index" "gatk_input_0" -p 'java -jar "$JAVA_JAR_PATH/GenomeAnalysisTK.jar" -T "UnifiedGenotyper" --num_threads ${GALAXY_SLOTS:-4} --out "/galaxy-repl/main/files/037/873/dataset_37873916.dat" --metrics_file "/galaxy-repl/main/files/037/873/dataset_37873917.dat" -et "NO_ET" -R "/galaxy/data/hg_g1k_v37/picard_index/hg_g1k_v37.fa" --genotype_likelihoods_model "BOTH" --standard_min_confidence_threshold_for_calling "30.0" --standard_min_confidence_threshold_for_emitting "30.0" '

 

 

Traceback (most recent call last):
  File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/unified_genotyper/66dd4d4c1743/unified_genotyper/gatk_wrapper.py", line 126, in <module>
    if __name__=="__main__": __main__()
  File "/cvmfs/main.galaxyproject.org/migrated_tools/toolshed.g2.bx.psu.edu/repos/devteam/unified_genotyper/66dd4d4c1743/unified_genotyper/gatk_wrapper.py", line 115, in __main__
    stderr_target.write( chunk )
TypeError: write() argument must be str, not bytes

 

0

• 

  SkyWarrior

  • February 21, 2020 05:56

  This is a galaxy wrapper fault not GATK.

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• 

  Mariano Avino

  • February 21, 2020 11:31

  ok thanks...I will try it locally with GATK

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