text: user4595: I am trying to run Mutect2 on a .bam file but I get an error by Googling can not be tackled
  Have you seen this error?
  fi1d18@RBGO-Server2:/data2/RNASeq/Angel/gatk$ ./gatk Mutect2 -R reference.fa -I sample.bam --germline-resource af-only-gnomad.hg38.vcf.gz --panel-of-normals pon.vcf.gz -O single_sample.vcf.gz
  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 Mutect2 -R reference.fa -I sample.bam --germline-resource af-only-gnomad.hg38.vcf.gz --panel-of-normals pon.vcf.gz -O single_sample.vcf.gz
  13:16:43.616 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
  Jan 31, 2022 1:16:43 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
  INFO: Failed to detect whether we are running on Google Compute Engine.
  13:16:43.733 INFO  Mutect2 - ------------------------------------------------------------
  13:16:43.734 INFO  Mutect2 - The Genome Analysis Toolkit (GATK) v4.2.4.1
  13:16:43.734 INFO  Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
  13:16:43.734 INFO  Mutect2 - Executing as fi1d18@RBGO-Server2 on Linux v4.15.0-166-generic amd64
  13:16:43.734 INFO  Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v11.0.13+8-Ubuntu-0ubuntu1.18.04
  13:16:43.734 INFO  Mutect2 - Start Date/Time: 31 January 2022 at 13:16:43 GMT
  13:16:43.734 INFO  Mutect2 - ------------------------------------------------------------
  13:16:43.734 INFO  Mutect2 - ------------------------------------------------------------
  13:16:43.735 INFO  Mutect2 - HTSJDK Version: 2.24.1
  13:16:43.735 INFO  Mutect2 - Picard Version: 2.25.4
  13:16:43.735 INFO  Mutect2 - Built for Spark Version: 2.4.5
  13:16:43.735 INFO  Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
  13:16:43.735 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
  13:16:43.735 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
  13:16:43.735 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
  13:16:43.735 INFO  Mutect2 - Deflater: IntelDeflater
  13:16:43.735 INFO  Mutect2 - Inflater: IntelInflater
  13:16:43.735 INFO  Mutect2 - GCS max retries/reopens: 20
  13:16:43.735 INFO  Mutect2 - Requester pays: disabled
  13:16:43.735 INFO  Mutect2 - Initializing engine
  13:16:44.015 INFO  Mutect2 - Shutting down engine
  [31 January 2022 at 13:16:44 GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.01 minutes.
  Runtime.totalMemory()=2155872256
  ***********************************************************************
  
  A USER ERROR has occurred: Cannot read file:///data2/RNASeq/Angel/gatk/pon.vcf.gz because no suitable codecs found
  
  ***********************************************************************
  Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
  
  I also get this
  fi1d18@RBGO-Server2:/data2/RNASeq/Angel/gatk$ file pon.vcf.gz
  pon.vcf.gz: HTML document, ASCII text, with very long lines
  
  
  user492: Your input file pon.vcf.gz should be a gzip file, but from your file command it looks like it is an HTML file instead. Perhaps you downloaded the VCF file incorrectly?
  Here is what I get on a bona fide gzip file in Ubuntu:
  $ echo hi | gzip -c > hi.gz
  $ file hi.gz
  hi.gz: gzip compressed data, from Unix, original size modulo 2^32 3
  
  
original_text: 4595: <p>I am trying to run Mutect2 on a .bam file but I get an error by Googling can not be tackled</p>
  <p>Have you seen this error?</p>
  <pre><code>fi1d18@RBGO-Server2:/data2/RNASeq/Angel/gatk$ ./gatk Mutect2 -R reference.fa -I sample.bam --germline-resource af-only-gnomad.hg38.vcf.gz --panel-of-normals pon.vcf.gz -O single_sample.vcf.gz
  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 Mutect2 -R reference.fa -I sample.bam --germline-resource af-only-gnomad.hg38.vcf.gz --panel-of-normals pon.vcf.gz -O single_sample.vcf.gz
  13:16:43.616 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
  Jan 31, 2022 1:16:43 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
  INFO: Failed to detect whether we are running on Google Compute Engine.
  13:16:43.733 INFO  Mutect2 - ------------------------------------------------------------
  13:16:43.734 INFO  Mutect2 - The Genome Analysis Toolkit (GATK) v4.2.4.1
  13:16:43.734 INFO  Mutect2 - For support and documentation go to https://software.broadinstitute.org/gatk/
  13:16:43.734 INFO  Mutect2 - Executing as fi1d18@RBGO-Server2 on Linux v4.15.0-166-generic amd64
  13:16:43.734 INFO  Mutect2 - Java runtime: OpenJDK 64-Bit Server VM v11.0.13+8-Ubuntu-0ubuntu1.18.04
  13:16:43.734 INFO  Mutect2 - Start Date/Time: 31 January 2022 at 13:16:43 GMT
  13:16:43.734 INFO  Mutect2 - ------------------------------------------------------------
  13:16:43.734 INFO  Mutect2 - ------------------------------------------------------------
  13:16:43.735 INFO  Mutect2 - HTSJDK Version: 2.24.1
  13:16:43.735 INFO  Mutect2 - Picard Version: 2.25.4
  13:16:43.735 INFO  Mutect2 - Built for Spark Version: 2.4.5
  13:16:43.735 INFO  Mutect2 - HTSJDK Defaults.COMPRESSION_LEVEL : 2
  13:16:43.735 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
  13:16:43.735 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
  13:16:43.735 INFO  Mutect2 - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
  13:16:43.735 INFO  Mutect2 - Deflater: IntelDeflater
  13:16:43.735 INFO  Mutect2 - Inflater: IntelInflater
  13:16:43.735 INFO  Mutect2 - GCS max retries/reopens: 20
  13:16:43.735 INFO  Mutect2 - Requester pays: disabled
  13:16:43.735 INFO  Mutect2 - Initializing engine
  13:16:44.015 INFO  Mutect2 - Shutting down engine
  [31 January 2022 at 13:16:44 GMT] org.broadinstitute.hellbender.tools.walkers.mutect.Mutect2 done. Elapsed time: 0.01 minutes.
  Runtime.totalMemory()=2155872256
  ***********************************************************************
  
  A USER ERROR has occurred: Cannot read file:///data2/RNASeq/Angel/gatk/pon.vcf.gz because no suitable codecs found
  
  ***********************************************************************
  Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
  </code></pre>
  <p>I also get this</p>
  <pre><code>fi1d18@RBGO-Server2:/data2/RNASeq/Angel/gatk$ file pon.vcf.gz
  pon.vcf.gz: HTML document, ASCII text, with very long lines
  </code></pre>
   492: <p>Your input file <code>pon.vcf.gz</code> should be a gzip file, but from your <code>file</code> command it looks like it is an HTML file instead. Perhaps you downloaded the VCF file incorrectly?</p>
  <p>Here is what I get on a bona fide gzip file in Ubuntu:</p>
  <pre class="lang-bash prettyprint-override"><code>$ echo hi | gzip -c &gt; hi.gz
  $ file hi.gz
  hi.gz: gzip compressed data, from Unix, original size modulo 2^32 3
  </code></pre>
  