Cannot run Makefit.R

[kaltinel]

Hi,
I am trying to run your snakemake,but I am doing it not from the very start as I already completed my mappins etc. At the moment, I am trying to fit my RNAseq Rcounts and therefore, I am trying to run Makefit.R.
My command line is:
Rscript MakeFit.R merged_RNASEQ_ncount.RData NULL fit_Rnaseq.RData '1:40' "24:25,25:26,23:24" 'simple'

However, I keep having an error of:

Error in `[.data.frame`(ncount, , fit.inter[1]) : 
  undefined columns selected
Calls: MakeFit -> paste0 -> [ -> [.data.frame
Execution halted

I looked for it, and saw that in similar issues the solution was to realize that there is a comma missing.
If I only provide "24:25" in commandline, instead of "24:25,25:26,23:24", it was running without errors for ~18 hours' and then it was stopped with the error of:

Error in IRLS(lp, control) :
  Number of iterations exceeded maximum MXITER = 400
Calls: MakeFit -> glm4 -> fitGlm4 -> IRLS
Execution halted

I would appreciate your help. Thank you!

[cgob]

Hello, Thanks for your message. Are you trying to run this command line outside of snakemake or trough a snakemake command/pipeline? The interpretation by python (snakemake) or bash of the quotation mark is not the same. Nevertheless, only one interaction term of codon pairs is fitted at once: 24:25 or 25:26 or 23:24 Although you have already completed your mapping, you can still run the pipeline using snakemake command. Just be careful that the name of the bam files match the sample spreadsheet. For the fit, you need a lof of memory (RAM) and I would advise to run it on a high computing cluster. Best, Cédric On 15 Jul 2020, at 01:09, kaltin <notifications@github.com<mailto:notifications@github.com>> wrote: Hi, I am trying to run your snakemake,but I am doing it not from the very start as I already completed my mappins etc. At the moment, I am trying to fit my RNAseq Rcounts and therefore, I am trying to run Makefit.R. My command line is: Rscript MakeFit.R merged_RNASEQ_ncount.RData NULL fit_Rnaseq.RData '1:40' "24:25,25:26,23:24" 'simple' However, I keep having an error of: Error in `[.data.frame`(ncount, , fit.inter[1]) : undefined columns selected Calls: MakeFit -> paste0 -> [ -> [.data.frame Execution halted I looked for it, and saw that in similar issues the solution was to realize that there is a comma missing. If I only provide "24:25" in commandline, instead of "24:25,25:26,23:24", it is running without errors. I would appreciate your help. Thank you! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#1>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AHWDQNPAVHQZA5NZYS3HBELR3TQQ3ANCNFSM4OZ7FO7Q>.

[cgob]

Hello,
Did you solve your issue?

Cédric

[Qiuying2019]

Hello,
I am trying to run your snakemake command/pipeline with your samples. And hit this R error at the Makefit step showing below:
Error in validObject(.Object) :
invalid class “dsparseModelMatrix” object: superclass "Mnumeric" not defined in the environment of the object's class
Calls: MakeFit ... initialize -> callNextMethod -> .nextMethod -> validObject
Execution halted

Any help on this issue?
Best,
Qiuying

[cgob]

Dear Qiuying,

Sorry for the late reply. Did you solve your issue ? Were you able to run the pipeline on your data successfully?

Best,

Cédric