![]() The second line has 2 red vertical line segments and a purple circle. The first line has one vertical line segment and a purple circle. Each line begins with the gray primer and then is joined by a red line segment with a vertical line attached that ends with a colored circle. At the tip of the arrow are 9 parallel lines, each increasing in length. At the point where the arrow from the key joins the arrow from the primer, the arrow is labeled primer extension and chain termination. The symbols for the key are ddTTP is red circle, ddCTP is blue circle ddATP is green circle and ddGTP is purple circle. The arrow is joined by an arrow from a key that read dNTPs. An arrow points from the primer to a series of horizontal lines that are increasing in length. Above the green line is a horizontal gray line with 9 small vertical lines extending from it the left side of the gray line is labeled 5 prime and the right side is labeled 3 prime and the line is titled primer. The left side of the line is labeled 3 prime, the right side of the line is labeled 5 prime, and the line is titled template. At the top of the diagram is a horizontal green line with 17 small vertical lines extending from the horizontal line. Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (-java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.A diagram with images showing the Sanger DNA sequencing method. ![]() ![]() Warning: DepthOfCoverage is a BETA tool and is not yet ready for use in productionġ1:51:35.506 INFO DepthOfCoverage - Initializing engineġ1:51:36.355 INFO FeatureManager - Using codec IntervalListCodec to read file file:///Volumes/My%20Passport%20for%20Mac/Experiments-%20raw%20data/1041%20WGS%20Kate_MN%20sequencing%20experiments_20210917/20200409_Sequencing%20IR%20MN%20HeLa_Novogene_rep1/WGS_202004/hg38.interval_listġ1:51:36.513 INFO IntervalArgumentCollection - Processing 2982123250 bp from intervalsġ1:51:36.526 INFO DepthOfCoverage - Done initializing engineġ1:51:36.662 INFO ProgressMeter - Starting traversalġ1:51:36.663 INFO ProgressMeter - Current Locus Elapsed Minutes Loci Processed Loci/Minuteġ1:51:36.671 INFO DepthOfCoverage - Shutting down engine EDTġ1:51:35.501 INFO DepthOfCoverage -ġ1:51:35.503 INFO DepthOfCoverage - HTSJDK Version: 2.24.1ġ1:51:35.503 INFO DepthOfCoverage - Picard Version: 2.27.1ġ1:51:35.503 INFO DepthOfCoverage - Built for Spark Version: 2.4.5ġ1:51:35.503 INFO DepthOfCoverage - HTSJDK Defaults.COMPRESSION_LEVEL : 2ġ1:51:35.503 INFO DepthOfCoverage - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : falseġ1:51:35.503 INFO DepthOfCoverage - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : trueġ1:51:35.503 INFO DepthOfCoverage - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : falseġ1:51:35.503 INFO DepthOfCoverage - Deflater: IntelDeflaterġ1:51:35.503 INFO DepthOfCoverage - Inflater: IntelInflaterġ1:51:35.504 INFO DepthOfCoverage - GCS max retries/reopens: 20ġ1:51:35.504 INFO DepthOfCoverage - Requester pays: disabled Java e_async_io_read_samtools=false e_async_io_write_samtools=true e_async_io_write_tribble=false pression_level=2 -jar /Applications/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar DepthOfCoverage -R hg38.fasta -I IR_MN_3.final.bam -O DepthOfCoverage -L hg38.interval_listġ1:51:35.169 INFO NativeLibraryLoader - Loading libgkl_compression.dylib from jar:file:/Applications/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar!/com/intel/gkl/native/libgkl_compression.dylibġ1:51:35.497 INFO DepthOfCoverage -ġ1:51:35.498 INFO DepthOfCoverage - The Genome Analysis Toolkit (GATK) v4.2.6.1ġ1:51:35.498 INFO DepthOfCoverage - For support and documentation go to ġ1:51:35.500 INFO DepthOfCoverage - Executing as on Mac OS X v11.4 x86_64ġ1:51:35.500 INFO DepthOfCoverage - Java runtime: Java HotSpot(TM) 64-Bit Server VM v16.0.2+7-67ġ1:51:35.501 INFO DepthOfCoverage - Start Date/Time: Jat 11:51:35 a.m. Using GATK jar /Applications/gatk-4.2.6.1/gatk-package-4.2.6.1-local.jar Gatk DepthOfCoverage -R hg38.fasta -I -O DepthOfCoverage -L hg38.interval_list dict file deleted from the directory) like this: Java -jar picard.jar CreateSequenceDictionary R=hg38.fasta O=hg38.dict I confirmed that "chr1_KI270762v1_alt" was present in the fasta file then used CreateSequenceDictionary to create a new sequence dictionary using:
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