Skip plot_coverage function [Feature request]

PubuduSaneth commented 4 years ago

plot_coverage function seems resource intensive and fails when cnv_facets is implemented in a nextflow process. Therefore it'll be quite useful to add a parameter to disable the plot_coverage function.

[2020-02-20 15:13:02] Loading file Px.FACETS.csv.gz...
[2020-02-20 15:14:42] Plotting histogram of coverage...
command.sh: line 2:    29 Killed                  cnv_facets.R -t Px.md.recal.bam -n Px.md.recal.bam -vcf dbsnp_146.hg38.vcf.gz -o Px.FACETS

dariober commented 4 years ago

Hi- Can you comment out the lines executing plot_coverage? It should be on line 817-818 in cnv_facets.R. Then execute again and see what happens and please let me know.

My guess is that if you run out of resources to make the plot than you'll run out also for the actual task of detecting CNVs, which should be more demanding. (I may be wrong though...)

Thanks Dario

PubuduSaneth commented 4 years ago

Hi,

Thank you very much for the quick reply. Yes, we have commented out plot_coverage lines in the cnv_facets.R script. This is working fine...

  #write(sprintf('[%s] Plotting histogram of coverage...', Sys.time()), stderr())
    # plot_coverage(rcmat= rcmat[['pileup']], rcmat_flt= rcmat_flt,
    # fname= paste0(xargs$out, '.cov.pdf'), title= paste0('Depth of coverage\n', xargs$out))

We are using the biocontainers cnv_facets image - quay.io/biocontainers/cnv_facets:0.15.0--r36h4b26f60_1 . So after modifying the R script in the container (from biocontainers/cnv_facets image), we commit those changes into a new docker image. This new docker image with modified cnv_facets.R script is functional in our NetFlow pipeline.

(Potentially, in a future version) If it is possible to disable the plot_coverage function using a command-line parameter, users can directly implement that feature using biocontainers/cnv_facets docker image.

Again, thank you so much for creating and maintaining this very useful tool.

dariober commented 4 years ago

Hi- I included the option --no-cov-plot to skip the plotting of coverage plots in v0.16.0 which is now on bioconda. Thanks for reporting the issue! Let me know of any problems...

PubuduSaneth commented 4 years ago

Dear Dario,

It looks like libcrypto.so.1.0.0 is not installed in biocontainers cnv_facets:v0.16.0. I received the following error.

bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
Error in checkForRemoteErrors(val) : one node produced an error:
Error in computing snp pileup. Exit code 1 from execution of ./P23993.FACETS.csv.gz_200319-031838_1d23a9455d/snp_pileup.chr1.sh
Calls: exec_snp_pileup_parallel ... clusterApply -> staticClusterApply -> checkForRemoteErrors

In addition to that is it possible to install fonts-conda-ecosystem fonts in the docker image. Fonts in png file (CNV plot) do not appear properly.

Again, thank you so much for developing and maintaining cnv_facets tool

dariober commented 4 years ago

Hi- Thanks for your patience - I love conda but sometimes... grrrrr! This issue with libcrypto seems to be resurfacing.

I can reproduce the issue and I escalated the problem to the bioconda list (https://github.com/bioconda/bioconda-recipes/issues/21229).

dariober commented 4 years ago

The issue with docker and bcftools should be fixed with the new recipe 0.16.0-1. This should work now:

docker run -it quay.io/biocontainers/cnv_facets:0.16.0--py38r36h4b26f60_1 bash

dariober / cnv_facets

Skip plot_coverage function [Feature request] #19