<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>

<gatk><picard><wes>
Getting error in running GATK
# Getting error in running GATK

(Asked by: username_0 on 2022-01-28)

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$

**Tags:** gatk, picard, wes

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## 0 answers

