A partical error for CNV_Stage7 .
Hi. I use GenomeSTRiP2.0, release of r1599, to call SV and CNV . I encountered a partical error during CNV_Stage7. INFO 10:03:48,179 HelpFormatter - Date/Time: 2015/07/08 10:03:48 INFO 10:03:48,180...
View ArticleSVPreprocess MergeInsertSizeHistograms error
Hi, I'm getting an OutOfMemoryError heap space error running SVPreprocess on 50 BAMs (see attached log file). The error occurs with MergeInsertSizeHistograms, which, if I understand the following forum...
View ArticleEM estep failed correction: 40 40.33333333333334
I have a question in a previous post. http://gatkforums.broadinstitute.org/discussion/5794/a-partical-error-for-cnv-stage7#latest I wonder whether the cause of error is associated about the specific...
View ArticleSamtools index error when running Preprocessing on GenomeStrip Release...
Hi, I am running GenomeStrip Release 2.00.1.602. I did the installtest run and everything works fine. Currently, I am working on 17 WGS bam files and I am constantly getting the following error. Error:...
View ArticleRemove samples from pre-processed metadata
Hi quick question regarding the SVPreprocess and generation of metadata. What is the quickest/most convenient way to filter out samples from the metadata contained in a single folder without having to...
View ArticleSVPreprocess error in SVToolkit version 2.00 (build 1602)
Hi, I got this error when I running SVPreprocess. GenomeInterval is 'chr07:8802402-9472402'. Error massage: Processing IRIS_313-7689/IRIS_313-7689_FCD0RHKACXX_L2/null ... Processing...
View ArticleGenomeSTrip+Queue+SGE
Hi, We're trying to use GenomeStrip 2.0 on our Sun Grid Engine. Genomestrip itself works but there are problems with Queue. We've tried to configure the shellscripts discover.sh and genotyping.sh by...
View Articlegender.map file about non-human species
I am deal with Drosophila SV with GenomeSTRiP. The DNA is extracted from pools of individuals,which makes it nearly impossible to know the gender of each sample.So how could I deal with gender.map that...
View ArticleError in SVPreprocess: "Unable to access log file"
Trying to run SVPreprocess, and I keep hitting the same "Unable to access log file" error. The log folder appears to be specified correctly, and in fact the program creates this folder itself, so it...
View Article"Could not find or load main class", but my classpath looks correct
Trying to run SVPreprocess; I am getting "Could not find or load main class" on the SVCommandLine class. My setup looks correct to me, so I am hoping for some advice. Sanity checks: $ java -version...
View Articlesample_gender.report.txt file is empty
I am getting a large number of errors like this from SVPreprocess: SVQScript-1000.out:Exception in thread "main" org.broadinstitute.sv.commandline.ArgumentException: Gender map file not found:...
View ArticleSV discovery batching
Dear Bob, we've recently seen in a project of 96 samples (all ~30x) that we get a very broad range of number of calls per sample (~600-900 deletions from SVdiscovery, using only PASS calls and removing...
View Articleconfidence interval around the breakpoints
I noticed that GenomeSTRiP use split-read to call deletion,so supposedly the breakpoints that GenomeSTRiP reports should be accurate.How anyone know that confidence interval of the breakpoints? Thanks...
View ArticleGenomeSTRiP installtest error
Hi, I just installed genomestrip version 2.00.1602. I tried to run the installation test. discovery.sh ran successfully, but genotyping.sh failed with error. The following are the error messages: INFO...
View ArticleSVGenotyper Error: Insert Size Record
I have a list of SVs from the 1kg phase3 VCF file that has been reduced to CNVs. The VCF file has the first 8 columns of the original from 1kg. I want to use 27 high coverage genomes from 1kg on my...
View ArticleError in GenomeStrip when using a bam file with added RG groups using...
Hi I have a question regarding the PicardTools AddOrReplaceReadGroups tool. I am using a single-sample WGS dataset and it arrived without any RG information, which I have now added with this command:...
View Articlewhat does '-disableGATKTraversal' mean ?
Hi. I want to know what 'disableGATKTraversal' mean. This is not described anywhere in this usage. If I Add '--disableGATKTraversal' to my scripts(i.e. SVPreprocessing, SVDiscovery, SVGenotyping,...
View ArticlesvGenotyper Error: Null Pointer
SVpreprocess seemed to run without error for my samples. However I'm getting an error with svGenotyper ##### ERROR...
View ArticleWhile running GenomeSTRIP preprocessing step the pipeline crushes:...
SVPreprocess-11.out and SVPreprocess-13.out are showing this error. Cannot build RC cache for empty readGroup list. ERROR stack trace java.lang.RuntimeException: Cannot build RC cache for empty...
View ArticleAbout SVAnnotation
Hi. I call structure variation and CNV using GenomeSTRiP2.0 , and I plan to apply annotation to my sv result. I want to use "-A GeneOverlap" but I can't find related files such as...
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