CNVdiscovery 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 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 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...
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 ArticleI need some tips to run GenomeSTRiP - CNVDiscovery
Hi, I'm trying to call CNVs by GenomeSTRiP software. As I know, I should run SVpreprocess first and CNVDiscovery second. So I tried SVpreprocess but It won't work. The errer said they need more option...
View Article"java.lang.NullPointerException" error
Dear developers, So recently I encountered "java.lang.NullPointerException" error, when dealing with 400+ samples in the SVDiscovery step. It was divided into 300+ jobs, and about 30 jobs failed due to...
View ArticleCNVDiscoveryPipeline fails at Stage5 -- no warn messages
Hi I'm using Genome STRiP CNVDiscoveryPipeline (v2.00.1833) on WGS data from a collection of inbred maize lines. I have populated the metadata directory to the best of my ability and was able to get...
View ArticleWindow size for samples of varying coverage
The documentation of the CNVDiscoveryPipeline makes it clear that several run parameters should be adjusted based on sequencing coverage. My samples are of variable coverage, but generally fall into 3...
View ArticleCNVDiscovery Errors at Stage 7 (at...
Hi Genome STRiP users, I met errors during running CNVDiscovery (latest Genome STRiP, 2.00.1833) on an LSF 9.X system with loading Drmaa. I started an interactive session on the cluster with requesting...
View ArticleGenomeSTRIP and Slurm
Hi Wusheng, A few words regarding your question about running genomeSTRIP on a cluster with a SLURM scheduler (I am using slurm 17.02.7). Here is what I understood, and I hope someone will correct me...
View ArticleSVPreprocess succeeded for fewer samples, but failed for large number of samples
``Hi Genome STRiP users, I am stuck on the step SVPreprocess. At first, I tried to run SVPreprocess with regards to 30 samples. The script I used is here. (To submit the job on the cluster, I requested...
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 ArticleSVDiscovery Error: GC overhead limit exceeded
Dear Genome STRiP users, I am running SVDiscovery with regards to 3418 sample (SVPreprocess completed without any errors) with the following script: module purge module load r/3.5.0 module load...
View ArticleError when running SVCNVDiscovery in batch-like way: Read count cache file is...
Dear Genome STRiP users, I am running SVCNVDiscovery process in a batch-like way. To be precisely, I have 3418 samples, and I divided them into 33 batches: the first 32 batches with 100 samples each...
View ArticleGATK 4 version still have some problems with asterisk in the VCF files.
Dear GATK team, I had used GATK 4 and GATK 3 best proctices to run WES data. BAM->gvcf->joint variant detection, VCF file->VQSR and so on. I noticed that in the GATK offical website, you...
View ArticleHow to Merge the Variants (and other data) if I run the CNVDiscovery &...
Dear Genome STRiP users, I successfully completed the SVCNVDiscovery pipeline in an individual running for the whole 3418 samples and got 29 variants or regions. But when I tried to run the...
View ArticleHow to pre-assign the multiple regions I want to process in each pipeline?
Dear Genome STRiP users, I intend to process part of the chromosome in each pipeline rather than processing the whole sequence. I know there is an -L flag in the SVPreprocess, but it is not listed in...
View ArticleError when running CNVDiscovery in a batch-like way: “Read count cache file...
Dear Genome STRiP users, I am running CNVDiscovery pipeline in a batch-like way, and always fail in No.4 batch, and No.23 batch with the following error: INFO 02:38:02,459 RefineCNVBoundaries -...
View Articlegenomestrip throws unhelpful slurm error when using the slurm-drmaa bridge
I am using the SLURM-DRMAA bridge and the pipeline throws an obstinate error. The obstinate error is "org.ggf.drmaa.InternalException: slurm_submit_batch_job: Invalid account or account/partition...
View ArticleSVPreprocess Error: failed to open "md_tempdir/headers.bam" No such file or...
Dear Genome STRiP users, I am running SVPreprocess to the range chr16:171000-178000. The SVPreprocess pipeline script is here...
View ArticleSVGenotyper error: Cannot get platform for read
I saw the other recent post regarding bam header issues in SVDiscovery, but thought I would post a separate question since this regards a separate script. I've run the CNVDiscovery pipeline on a set of...
View ArticleGenomeStrip query : SVDiscoveryWalker null pointer error
Dear all We've run into a problem when running the SV Discovery Step. The problem is likely to be something we did wrong a prior step and we'd be very grateful for any advice on trying to work out...
View ArticleGet Registered IELTS certificates without attending the...
PURCHASE/OBTAIN/GET/GAIN ORIGINAL IELTS,TOEFL,NEBOSH,GRE,TOEIC,PTE, FCE, CAE, CPE, BEC,YLE, KET,BULATS,ILEC, ICF certificates. skype id...(john dawson00)IELTS stands for “International English Language...
View ArticleSVDiscovery yielding far greater than expected number of polymorphic sites
Hi Bob, I ran SVPreprocess and SVDiscovery on a couple of loci in the human genome, each about 2 Mb in size, using high-coverage WGS data from 200 samples aligned to hg38 as input. One locus has...
View ArticleSVPreprocess Error: Alignment file does not exist
Dear Genome STRiP users, I completed SVPreprocess to certain cohort successfully. Now I apply the same script to another cohort for calling the same variants. However, a kind of unexpected errors...
View ArticleSVCNVDiscivery Error: "Caused by: java.lang.NullPointerException"
Dear Genome STRiP users, I completed SVCNVDiscovery to certain cohort based on the interval list: 1-500000. However, when I changed the interval list to 151000-198000, the error below poped up: ERROR...
View ArticleIs there any "pre copy number" value in the processing?
Dear Genome STRiP users, I completed the SVCNVDiscovery process to a certain cohort, and also calculate the copy number by other software such as Lumpy. But when I compare these two copy number...
View ArticleGenomeSTRiP query: Empty seq_1.merged.sites.vcf.gz file in Stage 3 of...
Dear all, While running the CNVDiscovery pipeline, we have found that the seq_1.merged.sites.vcf.gz file which is outputted by Stage 3 is empty. The CNVDiscovery pipeline does continue to run, however,...
View ArticleIs it possible to use vcf file as the input of the GenomeSTRiP?
Dear GenomeSTRiP users, I am using Genome STRiP for the cohorts that I only have the bcf or vcf files. Is there anyway to use the vcf files as the input to Genome STRiP? Because I rarely saw people can...
View ArticleSVPreprocess Error: java.lang.OutOfMemoryError
Dear Genome STRiP users, I can successfully complete SVPreprocess to 3418 samples. However, when I enlarge the sample size to 10686, it returned an error as below and it seems like that the even after...
View ArticleDifferent "java.lang.OutOfMemoryError: Java heap space" at nearly the end of...
Dear Genome STRiP users, I nearly completed the SVPreprocess to all 10686 samples: INFO 01:17:45,002 QGraph - 4 Pend, 2 Run, 0 Fail, 32076 Done However, I met a similar but not the same...
View ArticleSVCNVDiscovery Error "java.lang.OutOfMemoryError: Java heap space" AFTER...
Dear Genome STRiP users, I completed the SVPreprocess to the 10686 samples successfully. When I run SVCNVDiscovery pipeline with the following script,...
View ArticleSVCNVDiscovery Error: java.lang.RuntimeException: Read count cache file
Dear Genome STRiP users, I am running SVCNVDiscovery pipeline to 10686 samples with successfully completed SVPreprocesse. I met two "java.lang.RuntimeException" errors in the output. Exception in...
View ArticleIs the CNQ value the Phred quality score or the confidence percentile?
Dear Genome STRiP users, I completed the SVCNVDiscovery to all the samples in a single batch. Beside of the CN, I also got the CNQ for the CN of each sample. Based on...
View ArticleHow to Understand SVCNVDiscovery result: CN "-1" value with CNQ "." value
Dear Genome STRiP users, I got the CN and CNQ value by SVCNVDiscovery. After sorting the CNQ and the corresponding CN value, I found some weird CN values and CNQ values as below -- 10 samples out of...
View ArticleStrategies used by Genome Strip to detect CNVs
Dear all, I'm only want to know which strategies are used by Genome Strip in order to detect the CNVs... I looking for in the Genome Strip web page but I'm not sure... I saw in different papers where...
View ArticleERROR Stack trace: java.lang.NumberFormatException: For input string:...
Hi- I am working with GenomeSTRiP v2.0 on some bovine samples. Java is version 1.8.0_201. I created my own reference ploidy map as discussed on the Reference Genome Metadata page using the locations...
View ArticleDoes anyone know how long the GenomeSTRiP page is going to be down?
I was in the middle of working on something and had an error about missing commands but I can't check because the website was down! I have a deadline and so was wondering if you know how long it will...
View ArticleCNVDiscovery Stage 7 errors
Dear all We have run into a problem while running CNVDiscovery. The errors are occurring during Stage 7. An example of the type of error can be seen below: ERROR 00:13:56,742 FunctionEdge - Error:...
View ArticleCNV discovery pipeline
Hi, I am a new genome strip user, I just wanted to find out how does the CNV discovery pipeline work. I am having problems with understanding the 12 steps. I tried using the example given in the...
View ArticleCNVPipeline stage 7 error (unable to read the list of metadata directories)
I ran into this issue with reading metadata location when running CNVPipeline. I have 4 metadata directories, so I put their locations into a list called metadata.list The error message below can be...
View ArticleGenomeSTRip no genotype vcf
Dear all, I am calling SVs for WGS using the GenomeSTRiP tool. The calling is finished sucessfully for some chromosomes, but just only discovery vcf were generated for other chromosome. I run scripts...
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