How to use the background population sample?
I have some doubt about Genome STRiP software. As we all know:To run discovery or genotyping on a single sequenced genome or a small set of genomes, you need to call your data against a background...
View ArticleSVDiscovery error: computeSampleDoubleMap
I have encountered a problem when I run SVDiscovery pipeline. # # # The script of SVDiscovery I had used is: !/bin/bash export SV_DIR=/work/SoftW/svtoolkit runDir=2016006L-3-1...
View ArticleInformation about the result of CNVDiscoveryPipeline
@bhandsaker hi Bob,I got the result of CNVDiscoveryPipeline In the vcf file: SVTYPE=CNV,How could I known this CNV is belong to DEL or Dup? and if it is Dup,how many times the CNV repeat? and what are...
View ArticleAbout the result of CNVDiscoveryPipeline
@bhandsaker This is the CNV result of my test: gs_cnv.genotypes.vcf.gz # But I have some doubt: 1. How can I select the CNV which belong to my test sample (there are so many background population)...
View ArticleElapsed time about the CNVDiscoveryPipeline
@bhandsaker Hi Bob,why does the CNVDiscoveryPipeline is so time consuming? I test a WGS sample (about 30x),and run about 4 days,and it is still runing.This is my script about the CNVDiscoveryPipeline:...
View ArticleUnable to determine status of job ID error
Hi, I occasionally get the following type of error when using genome strip CNVDisvovery pipeline on a cluster running SGE, it will run successfully for long periods of time and then arrive at this type...
View ArticleA GATK RUNTIME ERROR, Invalid alignment found, alignmentStart > alignemntEnd
Hi, I was in the second step of Genome STRiP, to discover SV. It seems that all "partition" jobs worked fine, except one. The error message looks like this: ERROR 00:12:01,906 FunctionEdge - Contents...
View ArticleCNVdiscovery pipeline: Argument with name '--genderMapFile /'--ploidyMapFile'...
I'm testing the CNVdiscovery pipeline on a small set of individuals and I can't seem to get it running. I keep getting the following error despite both the gender & ploidy map being an optional...
View ArticleUnable to run SVPreprocess. Java cannot find the main class
Hello. I'm sure this is obvious but I can't seem to find my bug. I have been trying to execute the commands as listed in the documentation for our data but I am thwarted at every turn. Here are the...
View ArticleSVPreprocess Mismatch found between genome mask and reference
Hello. I'm trying to execute the SVPreprocess step on 48 samples I have. I've gotten the program to run but two of the SVPreprocesss*.out files contain errors/run failures. In one: SVPreprocess-5.out...
View ArticleEnable multithreading in genomeSTRiP
Hi Is there a way in genomeSTRiP to enable specify the number of threads the program can utilize? I've got a 56-core server and would like to maximize my usage of the available resources for...
View ArticleGenomeSTRiP v2.0 CNV calling
Hi Bob, I upgraded to version 2 and ran my samples with a 30 background population samples from 1000G for DEL discovery. I know that SVToolkit now calls deletions and copy number variation, my question...
View ArticleSlow in running Genome STRiP
I have such issue for a while, but I am not sure whether this is just the nature of the Genome STRiP software. In the preprocessing step, at first multiple small jobs will be submitted to the queue,...
View ArticleError running GenomeSTRiP --RCCache: index file is truncated: for...
When running gs_preprocess.sh, I am getting the error "index file is truncatated" on a number of files. Any suggestions for dealing with this? Is there a command to reindex the file? ERROR 13:50:58,287...
View Article[INSTALLTEST] Discovery.sh --> VCF is missing
Hi everyone I tried to launch the install test script (discovery.sh). All seems to work : no error in the logs, no error in the stderr. But at the end, I have this message : INFO 10:29:26,082...
View ArticleHow do you know when SVPreprocess has successfully finshed?
I apologize in advance if this is a stupid question. I'm coming from the world of gotcloud where when a step in the pipeline finishes a file called all.done gets created for that step. So in the event...
View ArticleInvalid intervals error
Hi, I'm currently working with Genomestrip (version 3.7.GS-r1748-0-g74bfe0b) to do some structural variant calling on some BAMs that were aligned to hg38. Naturally, I used the resources available from...
View Article"Unable to determine status of job" warn in Genome STRiP preprocessing
So when in the preprocessing step, there always occurs such kind of warning: WARN 10:50:19,392 DrmaaJobRunner - Unable to determine status of job id 2231784 org.ggf.drmaa.DrmCommunicationException:...
View ArticleSVPreprocess ERROR
Hi: I'm using Genome STRIP to call SV on my 5 test bam file, but on the first step--SVPreprocess, it has a error. The error looks no big deal, but when I keep on the second step--SVDiscovery, it can't...
View ArticleCNVDiscovery pipeline no ".done" file ?
Hi staff, In the CNVDiscovery pipeline working directory "cnv_stage2", seq_chr2 always restart all the jobs when I redo the pipeline, unlike other chromosomes. I checked the seq_chr2 folder, even...
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