Potential Problems with BAM file header, r package input, or RNASeq data pipeline

Question

[ss650012]

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20180719 12:23:24 - E:'brglm' will gradually be superseded by 'brglm2' (https://cran.r-project.org/package=brglm2), which provides utilities for mean and median bias reduction for all GLMs and methods for the detection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!

[h.mon]

What does the log file ( /Users/as/GLMVC/rep1_r1.tsv.r.log ) says?

Did you try manually running the script "/Users/as/GLMVC/rep1_r1.tsv.r", as the error message suggested?

[KG]

Followed your advise and ran R script manually and unfortunately I am getting error

No lines are available for input I believe this error is being produced because I think GLMVC suppose to make input for the Read Table R package internally. In order to produce this file GLMVC run samtools Mpileup method after running this function manually on the files I receive

[mpileup] 2 samples in 2 input files

is this correct I am unsure since the file which is outputed does not seem to be right. Please help.

Thanks in advance