<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>

CC BY-SA 4.0
2022-01-31T15:22:17.127Z
Thank you, you were right, I downloaded the proper file but I get the same error, please have a look at my main post]
Zizogolu
CC BY-SA 4.0
2022-01-31T13:57:38.133Z
2022-01-31T13:57:38.133Z
winni2k
<p>Downloading that vcf file from this link fixes the problem (but generates a new one)</p>
<pre><code>wget https://storage.googleapis.com/gatk-best-practices/somatic-hg38/1000g_pon.hg38.vcf.gz
</code></pre>

CC BY-SA 4.0
2022-01-31T15:55:35.780Z
2022-01-31T18:43:47.647Z
2022-01-31T18:43:47.647Z
Zizogolu
<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>

CC BY-SA 4.0
2022-01-31T15:43:43.457Z
Sorry, I think the nature of stackexchange is such that you will need to post a new question to get help with the new problem. Perhaps a better location for this question is biostars? https://www.biostars.org/
winni2k
CC BY-SA 4.0
2022-01-31T18:45:59.370Z
Yep, edits are for clarification, questions can't be moving targets (I understand it's frustrating, but changing the question renders the answers obsolete and that just generates a mess - which is the reason we don't allow it here)
Kamil S Jaron
<gatk><mutations><wes>
Error in running Mutect2
# Error in running Mutect2

(Asked by: username_0 on 2022-01-31)

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

**Tags:** gatk, mutations, wes
> **Comments:**
> **username_1**: Sorry, I think the nature of stackexchange is such that you will need to post a new question to get help with the new problem. Perhaps a better location for this question is biostars? https://www.biostars.org/  
> **username_2**: Yep, edits are for clarification, questions can't be moving targets (I understand it's frustrating, but changing the question renders the answers obsolete and that just generates a mess - which is the reason we don't allow it here)  

---

## 2 answers

### Answer by username_1 on 2022-01-31. Score: 2

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

> **Comments:**
> **username_0**: Thank you, you were right, I downloaded the proper file but I get the same error, please have a look at my main post]  

---

### Answer by username_0 on 2022-01-31. Score: 1

Downloading that vcf file from this link fixes the problem (but generates a new one)
wget https://storage.googleapis.com/gatk-best-practices/somatic-hg38/1000g_pon.hg38.vcf.gz


---

