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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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Issue with facets execution #44

Open nsoriano2 opened 2 years ago

nsoriano2 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

Thanks @chrismacdermaid, I was going to suggest that.

nsoriano2 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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