Issue with facets execution

[nsoriano2]

Hello,

I have this message when I try to run cnv_facets :

Error in makeCluster(nprocs, type = "FORK") : 
  could not find function "makeCluster"
Calls: exec_snp_pileup_parallel
Execution halted

It looks like a R problem ?

I've installe cnv_facets using conda and according to your instructions in https://githubhot.com/repo/dariober/cnv_facets/issues/35

R --version
R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)

samtools --version
samtools 1.15
Using htslib 1.14
Copyright (C) 2022 Genome Research Ltd.

[chrismacdermaid]

load the parallel library near the other libraries being loaded at the top of the main R script.

library('parallel')

That fixed if for me. Same R version.

[dariober]

Thanks @chrismacdermaid, I was going to suggest that.

[nsoriano2]

Thanks to you both,

I finally reinstalled with mamba install without precising any version for the dependencies and it worked, out of the box. When I tried the same yesterday with conda, I had a lot of issues. Probaly a problem with the conda channels...

That's why I tried the instructions of issue 35.

cnv_facets is running on 17 samples right now :-)

(with a few warnings :

- [ ] - [ Warning message:
- [ ] package 'argparse' was built under R version 3.6.3 
- [ ] .Warning messages:
- [ ] 1: package 'facets' was built under R version 3.6.3 
- [ ] 2: package 'pctGCdata' was built under R version 3.6.3 
- [ ] .Warning message:
- [ ] package 'data.table' was built under R version 3.6.3 
- [ ] Warning message:
- [ ] package 'ggplot2' was built under R version 3.6.3 ] 

[nsoriano2]

Hello, I don't know why, but the problem reappeared... I've added the library line in cnv_facets.R and now it works.

But...

I've now a new problem on all my samples :

[2022-05-17 11:19:41] Plotting histogram of coverage... [2022-05-17 11:20:05] Preprocessing sample... [2022-05-17 11:20:08] Processing sample... Error in seg.start[seg]:seg.end[seg] : NA/NaN argument Calls: run_facets -> procSample -> jointsegsummary Execution halted

Something like a dvision by zero ? Any idea ?

[dariober]

Can you try to see if the test data run from start to finish? Just to see if the issue is with the installation or something unexpected with your data.

[nsoriano2]

Hi Dario,

I'll give a try to te test data when I'll be back home (I'm attending a congress). Is it the data I can find in te source folder on github : cnv_facets/test/data/ ?

[nsoriano2]

Hi Dario, I did the test with TCRBOA6 data and it ran flowessly. I'm having a close look at my data to find out why cnv_facets halts on all of them after completing the csv files...

Any idea ?

example of failure : Finished in 0.000000 seconds. Finished in 11.400000 seconds. Finished in 64.910000 seconds. Finished in 12.610000 seconds. [2022-06-09 17:59:13] Loading file 100-3.csv.gz... [2022-06-09 17:59:22] Plotting histogram of coverage... [2022-06-09 17:59:45] Preprocessing sample... [2022-06-09 17:59:49] Processing sample... Error in seg.start[seg]:seg.end[seg] : NA/NaN argument Calls: run_facets -> procSample -> jointsegsummary Execution halted