I am getting this error below and Summary and Off-targets file are not created. I would appreciate any suggestion.
Building feature vectors for scoring ... Calculating scores ... Error in `$<-.data.frame`(`*tmp*`, "score", value = c(0.0112619406241216, : replacement has 443126 rows, data has 443130
This the code below:
offTargetAnalysis(inputFilePath, REpatternFile = REpatternFile, scoring.method = "CFDscore", min.score = 0.000001, format = "fasta", findgRNAsWithREcutOnly = FALSE, # if FALSE not restr. enzymes findPairedgRNAOnly = FALSE, # paired only turn to FALSE if only WT Cas9 not Nickase gRNA.name.prefix = "g.", orgAnn = orgAnn, BSgenomeName = BSgenomeName, txdb = txdb, chromToSearch= "all", # change here for all to look at all chromosomes min.gap = 0, max.gap = 20, max.mismatch = 4, # changed on 11-26-18 to 4 from 3 topN = 1000, topN.OfftargetTotalScore= 10, # 10 top Offtarget will be calculated annotateExon = TRUE, fetchSequence = TRUE, upstream = 250, downstream = 250, overlap.gRNA.positions = c(17, 18), PAM.size = 3, PAM = "NGG", foldgRNAs = TRUE, gRNA.size = 20, outputDir = outputDir, overwrite = TRUE)
> attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods base > > other attached packages:  Hmisc_4.2-0 ggplot2_3.1.0 Formula_1.2-3 > survival_2.43-3 lattice_0.20-38 >  org.Hs.eg.db_3.7.0 > TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 > BSgenome.Hsapiens.UCSC.hg19_1.4.0 org.Mm.eg.db_3.7.0 > TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.4  GenomicFeatures_1.34.3 > AnnotationDbi_1.44.0 Biobase_2.42.0 > BSgenome.Mmusculus.UCSC.mm10_1.4.0 BSgenome_1.50.0 >  rtracklayer_1.42.1 GenomicRanges_1.34.0 > GenomeInfoDb_1.18.1 seqRFLP_1.0.1 > CRISPRseek_1.22.1  seqinr_3.4-5 > Biostrings_2.50.2 XVector_0.22.0 > IRanges_2.16.0 S4Vectors_0.20.1 >  BiocGenerics_0.28.0