Not output and not error from GATK CreateSequenceDictionary

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Marcela Martinez

• January 07, 2024 14:12

REQUIRED for all errors and issues:
a) GATK version used:
b) Exact command used:
c) Entire program log:

./gatk CreateSequenceDictionary \

        -R ${ref}Homo_sapiens_assembly38.fasta \

        -O ${ref}Homo_sapiens_assembly38.dict

to generate a dictionary for the reference genome, being ${ref}, the path to the genome fasta file

The script runs fine (without error), but it did not generate the output file (ref dictionary)

Using GATK jar /grupos/Marce/clinica/pipeline/tools/gatk4/gatk-4.2.5.0/gatk-package-4.2.5.0-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 /grupos/Marce/clinica/pipeline/tools/gatk4/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar CreateSequenceDictionary -R /grupos/Marce/clinica/pipeline/tools/GATK-CNVs/bundle/Homo_sapiens_assembly38.fasta -O /grupos/Marce/clinica/pipeline/tools/GATK-CNVs/bundle/Homo_sapiens_assembly38.dict

Any explanation would be very much appreciated.

Marcela

 

 

0

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  Michael Gatzen

  • January 11, 2024 14:53

  Hi Marcela,

  The command you posted should work without a problem. Is the output you posted the complete output? The last line should end with a line that says "Tool returned: 0". If it doesn't then that might be indicative that the program has been killed externally. Could you check that the command finishes?

  Thanks,
  Michael

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