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hartleys / QoRTs

Quality of RNA-Seq Toolset
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AUTO GENERATE PLOTS R SCRIPT NOT WORKING #78

Open mya2152 opened 4 years ago

mya2152 commented 4 years ago

Hi I finished running QoRTs on my aligned reads and then transferred the output files to my laptop. Upon opening the "QC.makeMultiplot.R" file I am greeted with some parameters relating to file locations etc which I proceed in changing as I've move my files to my laptop. However, once I try to run the script I get this error:

message("DONE..."); DONE... message("STARTING..."); STARTING... library(QoRTs); unique.ID <- c("ftp3013_KOA_xAligned"); qc.data.dir <- c("D:/D_Downloads/qc_collection/QoRTs_output/ftp3013_KOA_xAligned/"); qc.data.prefix <- c(""); decoder.raw <- data.frame(unique.ID = as.character(unique.ID), qc.data.dir = as.character(qc.data.dir), qc.data.prefix=as.character(qc.data.prefix),stringsAsFactors=FALSE); decoder <- completeAndCheckDecoder(decoder = decoder.raw) message(decoder); ftp3013_KOA_xAlignedD:/D_Downloads/qc_collection/QoRTs_output/ftp3013_KOA_xAligned/ftp3013_KOA_xAlignedUNKNOWNUNKNOWN message(lapply(names(decoder), function(n){ class(decoder[[n]]) })); charactercharactercharactercharactercharactercharacter res <- read.qc.results.data("", decoder = decoder, calc.DESeq2 = FALSE, calc.edgeR = FALSE); Note: no input.read.pair.count column found. This column is optional, but without it mapping rates cannot be calculated. Note: no multi.mapped.read.pair.count column found. This column is optional, but without it (depending on how your aligner implements multi-mapping) multi-mapping rates might not be plotted. WARNING: QoRTs run absent! Dir not found: D:/D_Downloads/qc_collection/QoRTs_output/ftp3013_KOA_xAligned/! Error in read.in.results.data.with.decoder(decoder = decoder.final, infile.dir = infile.dir, : Fatal error: QoRTs run data not found! Use autodetectMissingSamples = TRUE to automatically skip these runs

makeMultiPlot.basic(res, outfile = "D:/D_Downloads/qc_collection/QoRTs_output/ftp3013_KOA_xAligned/QC.multiPlot.pdf", plotter.params = list(std.color = "blue", std.lines.lwd = 4), plot.device.name = "pdf"); Error in build.plotter.basic.helper(res, res@decoder$lane.ID, compiled.params = compiled.params, : object 'res' not found

message("DONE..."); DONE...

I can't get any plots to generate because of this and there is no issue with accessing the file location.

ngualand commented 4 years ago

Hi you probably have a error in the decoder.txt file. The error should be that the name in the decoder file do not match with the name of the folder in the "QoRTs_output/" directory.