FilterMutectCalls
Hello,
I followed GATK best practice pipeline with RNAseq. I wanted to call somatic variants using Mutect2 and followed with FilterMutectCalls.
FilterMutectCalls was done successfully, but it created output as *. vcf.gz?
I tried gatk/4.1.3.0 and gatk/4.1.7.0 and both version created same output file extension.
I could not use this output file in further step.
Do you have any suggestions?
Thank you.
At this moment only your /rsrch3/home directory is mounted.
15:21:10.301 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gatk/gatk-package-4.1.3.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Nov 11, 2020 3:21:10 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
15:21:10.474 INFO FilterMutectCalls - ------------------------------------------------------------
15:21:10.474 INFO FilterMutectCalls - The Genome Analysis Toolkit (GATK) v4.1.3.0
15:21:10.474 INFO FilterMutectCalls - For support and documentation go to https://software.broadinstitute.org/gatk/
15:21:10.474 INFO FilterMutectCalls - Executing as nozirmak@cdragon108 on Linux v3.10.0-693.el7.x86_64 amd64
15:21:10.474 INFO FilterMutectCalls - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_212-8u212-b03-0ubuntu1.16.04.1-b03
15:21:10.475 INFO FilterMutectCalls - Start Date/Time: November 11, 2020 3:21:10 PM UTC
15:21:10.475 INFO FilterMutectCalls - ------------------------------------------------------------
15:21:10.475 INFO FilterMutectCalls - ------------------------------------------------------------
15:21:10.475 INFO FilterMutectCalls - HTSJDK Version: 2.21.2
15:21:10.475 INFO FilterMutectCalls - Picard Version: 2.21.9
15:21:10.475 INFO FilterMutectCalls - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:21:10.475 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:21:10.475 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:21:10.475 INFO FilterMutectCalls - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:21:10.475 INFO FilterMutectCalls - Deflater: IntelDeflater
15:21:10.475 INFO FilterMutectCalls - Inflater: IntelInflater
15:21:10.475 INFO FilterMutectCalls - GCS max retries/reopens: 20
15:21:10.475 INFO FilterMutectCalls - Requester pays: disabled
15:21:10.475 INFO FilterMutectCalls - Initializing engine
15:21:13.569 INFO FeatureManager - Using codec VCFCodec to read file file:///rsrch3/home/ccp/vilarsanchez/rhesuslynch/STAR_2pass/SecondPass/GATK_RNA/mutect2/NOL1.merged.unfiltered.somatic.vcf.gz
15:21:16.843 INFO FilterMutectCalls - Done initializing engine
". Defaulting to VCF.TKVariantContextUtils - Can't determine output variant file format from output file extension "vcf
15:21:18.650 INFO ProgressMeter - Starting traversal
15:21:18.650 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
15:21:18.651 INFO FilterMutectCalls - Starting pass 0 through the variants
15:21:25.578 INFO FilterMutectCalls - Finished pass 0 through the variants
15:21:53.273 INFO FilterMutectCalls - Starting pass 1 through the variants
15:21:53.344 INFO ProgressMeter - 1:5175684 0.6 119000 205799.3
15:21:59.491 INFO FilterMutectCalls - Finished pass 1 through the variants
15:22:08.500 INFO FilterMutectCalls - Starting pass 2 through the variants
15:22:08.556 INFO ProgressMeter - 1:8438136 0.8 238000 286137.9
15:22:14.796 INFO FilterMutectCalls - Finished pass 2 through the variants
15:22:14.830 INFO FilterMutectCalls - Starting pass 3 through the variants
15:22:18.604 INFO ProgressMeter - 6:110252768 1.0 398000 398305.4
15:22:24.503 INFO FilterMutectCalls - Finished pass 3 through the variants
15:22:24.509 INFO FilterMutectCalls - No variants filtered by: AllowAllVariantsVariantFilter
15:22:24.510 INFO FilterMutectCalls - 0 read(s) filtered by: AllowAllReadsReadFilter
15:22:24.510 INFO ProgressMeter - JSUE03217332.1:4881 1.1 474940 432681.4
15:22:24.510 INFO ProgressMeter - Traversal complete. Processed 474940 total variants in 1.1 minutes.
15:22:24.954 INFO FilterMutectCalls - Shutting down engine
[November 11, 2020 3:22:24 PM UTC] org.broadinstitute.hellbender.tools.walkers.mutect.filtering.FilterMutectCalls done. Elapsed time: 1.24 minutes.
Runtime.totalMemory()=9730785280
Using GATK jar /gatk/gatk-package-4.1.3.0-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 /gatk/gatk-package-4.1.3.0-local.jar FilterMutectCalls -R rheMac8.toplevel.fa -V NOL1.merged.unfiltered.somatic.vcf.gz --tumor-segmentation NOL1.segments.table --contamination-table NOL1.calculatecontamination.table --output NOL1.merged.filtered.somatic.vcf
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Nejla Ozirmak Lermi .gz is a zipped extension. If you wish to have the file unzipped, you can use many different methods to unzip the file. GATK does not have a tool to unzip it.
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Genevieve Brandt thank you for answering my question.
Actually the problem was output files that FilterMutectCalls created.
I copied " *.vcf.gz?" file as "*.vcf.gz" using cp command.
Then, annotation software accepted new files as input files and the program annotated the variants.
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Hi Nejla Ozirmak Lermi, could you verify that this issue exists in GATK 4.1.9.0 and also supply your complete command?
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Hi Genevieve Brandt, GATK 4.1.9.0 didn't exist in our server yet, thus I couldn't verify this issue in GATK 4.1.9.0. Complete command is below.
gatk FilterMutectCalls -R rheMac8.toplevel.fa -V NOL7.merged.unfiltered.somatic.vcf.gz --tumor-segmentation NOL7.segments.table --contamination-table NOL7.calculatecontamination.table --output NOL7.merged.filtered.somatic.vcf.gz
Output files were NOL7.merged.filtered.somatic.vcf.gz?; NOL7.merged.filtered.somatic.vcf.gz?.idx; NOL7.merged.filtered.somatic.vcf.gz?.filteringStats.tsv
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Nejla Ozirmak Lermi I would like to try to verify this issue on my end. Please submit a bug report following these instructions including all necessary files for the script to run, the command in a text file, and the error message in a text file.
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