SVPreprocess 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 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 ArticleNo gender data for sample
Hi! I am trying to run the SVToolkit.2.00.1533 on rice ,which is a self-pollinated pants and has no genders.I got an error for" No gender data for sample". Because my samples ,rice, a self-pollinated...
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 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...
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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 ArticleOne plot error about CNVpipeline stage5
Hi, I met another error about GenomeStrip2.0 CNVdiscoveryPipeline, and it stopped at stage5. Some parts of the error log are as following, ERROR 09:59:48,040 FunctionEdge - Contents of...
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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...
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We(ieltssolution at outlook dot com) deal and specialize in the production of Original and registered IELTS/TOEFL/ESOL/GRE/PTE/GMAT/Nebosh/CELTA/DELTA & other English Language Certificates all are...
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