text: user4595: I am trying to making a fasta doc using GATK tools but I don't know what does this error say
  Server2:/data2/RNASeq/Angel/gatk$ ./gatk CreateSequenceDictionary -R reference.fa
      Using GATK jar /data2/RNASeq/Angel/gatk/gatk-package-4.2.4.1-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 /data2/RNASeq/Angel/gatk/gatk-package-4.2.4.1-local.jar CreateSequenceDictionary -R reference.fa
      INFO    2022-01-28 15:04:19 CreateSequenceDictionary    Output dictionary will be written in reference.dict
      15:04:19.401 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data2/RNASeq/Angel/gatk/gatk-package-4.2.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
      [Fri Jan 28 15:04:19 GMT 2022] CreateSequenceDictionary --REFERENCE reference.fa --TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
      Jan 28, 2022 3:04:19 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
      INFO: Failed to detect whether we are running on Google Compute Engine.
      [Fri Jan 28 15:04:19 GMT 2022] Executing as Server2 on Linux 4.15.0-166-generic amd64; OpenJDK 64-Bit Server VM 11.0.13+8-Ubuntu-0ubuntu1.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.2.4.1
      [Fri Jan 28 15:04:19 GMT 2022] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
      Runtime.totalMemory()=2155872256
      To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
      picard.PicardException: /data2/RNASeq/Angel/gatk/reference.dict already exists.  Delete this file and try again, or specify a different output file.
          at picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:220)
          at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
          at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)
          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)
      Server2:/data2/RNASeq/Angel/gatk$
  
  user-1: picard.PicardException: /data2/RNASeq/Angel/gatk/reference.dict already exists.  Delete this file and try again, or specify a different output file.
  
  I think that requires no further explanation.
  
original_text: 4595: <p>I am trying to making a fasta doc using GATK tools but I don't know what does this error say</p>
  <p>Server2:/data2/RNASeq/Angel/gatk<span class="math-container">$ ./gatk CreateSequenceDictionary -R reference.fa
      Using GATK jar /data2/RNASeq/Angel/gatk/gatk-package-4.2.4.1-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 /data2/RNASeq/Angel/gatk/gatk-package-4.2.4.1-local.jar CreateSequenceDictionary -R reference.fa
      INFO    2022-01-28 15:04:19 CreateSequenceDictionary    Output dictionary will be written in reference.dict
      15:04:19.401 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/data2/RNASeq/Angel/gatk/gatk-package-4.2.4.1-local.jar!/com/intel/gkl/native/libgkl_compression.so
      [Fri Jan 28 15:04:19 GMT 2022] CreateSequenceDictionary --REFERENCE reference.fa --TRUNCATE_NAMES_AT_WHITESPACE true --NUM_SEQUENCES 2147483647 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
      Jan 28, 2022 3:04:19 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
      INFO: Failed to detect whether we are running on Google Compute Engine.
      [Fri Jan 28 15:04:19 GMT 2022] Executing as Server2 on Linux 4.15.0-166-generic amd64; OpenJDK 64-Bit Server VM 11.0.13+8-Ubuntu-0ubuntu1.18.04; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:4.2.4.1
      [Fri Jan 28 15:04:19 GMT 2022] picard.sam.CreateSequenceDictionary done. Elapsed time: 0.00 minutes.
      Runtime.totalMemory()=2155872256
      To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
      picard.PicardException: /data2/RNASeq/Angel/gatk/reference.dict already exists.  Delete this file and try again, or specify a different output file.
          at picard.sam.CreateSequenceDictionary.doWork(CreateSequenceDictionary.java:220)
          at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
          at org.broadinstitute.hellbender.cmdline.PicardCommandLineProgramExecutor.instanceMain(PicardCommandLineProgramExecutor.java:37)
          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)
      Server2:/data2/RNASeq/Angel/gatk$</span></p>
   -1: <pre><code>picard.PicardException: /data2/RNASeq/Angel/gatk/reference.dict already exists.  Delete this file and try again, or specify a different output file.
  </code></pre>
  <p>I think that requires no further explanation.</p>
  