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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
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    $\begingroup$ 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? biostars.org $\endgroup$ Commented Jan 31, 2022 at 15:43
  • $\begingroup$ 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) $\endgroup$ Commented Jan 31, 2022 at 18:45

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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
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    $\begingroup$ Thank you, you were right, I downloaded the proper file but I get the same error, please have a look at my main post] $\endgroup$ Commented Jan 31, 2022 at 15:22
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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
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