Hi, I am trying to make the GLMVC pipeline (https://github.com/shengqh/glmvc) work and am incurring a few issues. For this pipeline, you simply need to download the package and run it in the command line with two BAM files, one normal and one tumor. I have done that and am receiving the following error that is very persistent:
20180719 12:23:23 - filter process started at 07/19/2018 12:23:23 20180719 12:23:24 - E:Loading required package: profileModel 20180719 12:23:24 - E:'brglm' will gradually be superseded by 'brglm2' (https://cran.r-project.org/package=brglm2), which provides utilities for mean and median bias reduction for all GLMs and methods for the detection of infinite estimates in binomial-response models. 20180719 12:23:24 - E:Error in read.table(inputfile, header = T, stringsAsFactors = F) : 20180719 12:23:24 - E: no lines available in input 20180719 12:23:24 - E:Execution halted Error: R command failed to genearte result as /Users/as/GLMVC/rep1_r1.unfiltered.tsv. Check the log file /Users/as/GLMVC/rep1_r1.tsv.r.log. You can manully run the R script file /Users/as/GLMVC/rep1_r1.tsv.r to find out the problem. Trace: at RCPA.R.RProcessor.Process () [0x00219] in <2447b922059f4ad28c04638fa7048d73>:0 at CQS.Genome.SomaticMutation.FilterProcessor.Process () [0x00084] in <b7c50a2fd30542368a2470adaa3a0af4>:0 at CQS.Genome.SomaticMutation.PipelineProcessor.Process () [0x000e5] in <b7c50a2fd30542368a2470adaa3a0af4>:0 at RCPA.Commandline.AbstractCommandLineCommand`1[T].DoProcess (System.String args, System.Boolean result) [0x0005c] in <2447b922059f4ad28c04638fa7048d73>:0 at RCPA.Commandline.AbstractCommandLineCommand`1[T].Process (System.String args) [0x00015] in <2447b922059f4ad28c04638fa7048d73>:0
I have tried editing the BAM file header using Picard AddOrReplaceReadGroups, and I have ensured that all of my BAM files were processed using the same pipeline.
Any help would be appreciated.
Thank you so much in advance!