cgob / codondt_snakemake Goto Github PK

Hi Cyril,

Thanks for your work - codonDT has the potential to be quite useful for our work.

I have matched riboseq and rnaseq data. I've run a test sample with only the riboseq to completion. Now I'm trying to run both the RNA and Riboseq. And hit this R error.

Error in sparse.model.matrix(data = ncount, formu) : object 'formu' not found Calls: MakeFit -> sparse.model.matrix -> terms Execution halted [Fri Apr 30 19:44:11 2021] Error in rule makefit_combined: jobid: 138 output: Data/Fit/CHX7_RIBO_fit_24:25.RData, Data/Fit/CHX7_RIBO_fit_24:25.RData.pred, Data/Fit/CHX7_RIBO_fit_24:25.RData.cor

Best,
Colin

Hello, Cédric,
First, thanks for your nice work.
I want to run this script on my contos machine, but I can't run it successfully.
First, I download this repo by gh repo clone cgob/codonDT_snakemake and simply run the file running_command.sh.
But error occurred:

sbatch: error: fetch_config: DNS SRV lookup failed
sbatch: error: _establish_config_source: failed to fetch config
sbatch: fatal: Could not establish a configuration source

It's there anything I missed? Looking for your help.
Tanks again!

Eggs

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!

Hi,

I am having some troubles running the Makefit.R script on my RNA seq samples. I have 75 bp reads and when I used the the standard length filter preset in the config.yaml it would not create any count files for my RNA samples. This I could fix by setting the upper limit (L2) to 75, which I already found a little odd. Shouldn't be the read length filter only be relevant to the Riboseq files? Do I have to do something to my RNA reads before feeding them into the pipeline, or am I just missing something?

Makefit.R is then throwing this error:

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

The RIBO files alone run through without a problem.

Thank you for your help!

Hello, I am currently using codonDT_snakemake to analyze my ribosome profiling data. The code will run without any errors and finish, but I am unable to find any output files. I am assuming the output files should be within the /Data/ directory? Any suggestions on how I can resolve this?