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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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Cluster execution halted error with "parallel" in R 4.1.0 version on RHEL8 machine. #42

Closed shivak3 closed 3 years ago

shivak3 commented 3 years ago

Hi,

I have installed cnv_facets using the setup script.

When I run the code, I am getting this error.

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

Please guide me if anyone come across this issue. -Thank you.

dariober commented 3 years ago

Hi- How did you install cnv_facets? I'm afraid cnv_facets needs R 3.x (I need to fix the conda recipe!). See also issue https://github.com/dariober/cnv_facets/issues/35. Unless you have a specific reason to do otherwise, do:

conda create -n cnv_facets
conda activate cnv_facets
mamba install -c bioconda -c conda-forge cnv_facets # Better to use mamba instead of conda
shivak3 commented 3 years ago

Hi Dariober,

Thank you for your reply.

I installed cnv_facets using setup script.

bash setup.sh --bin_dir </dir/on/path>

on my machine , its like

bash setup.sh --bin_dir /usr/local/bin

And, I am trying to run cnv_facets.R from terminal like

[test@rhel8 ~]# cnv_facets.R -v
0.16.0; facets=0.5.14
[test@rhel8 ~]# cnv_facets.R -h
usage: /usr/local/bin/cnv_facets.R [-h] --out OUT [--snp-tumour SNP_TUMOUR]
                                   [--snp-normal SNP_NORMAL]
                                   [--snp-vcf SNP_VCF] [--snp-mapq SNP_MAPQ]
                                   [--snp-baq SNP_BAQ] [--snp-count-orphans]
                                   [--snp-nprocs SNP_NPROCS] [--pileup PILEUP]
                                   [--depth DEPTH DEPTH] [--targets TARGETS]
                                   [--cval CVAL CVAL] [--nbhd-snp NBHD_SNP]
                                   [--annotation ANNOTATION]
                                   [--gbuild {hg19,hg38,mm9,mm10}]
                                   [--unmatched] [--no-cov-plot]
                                   [--rnd-seed RND_SEED] [-v]

Do you recommend the above installation and cnv_facets.R execution from terminal? OR You recommend it using only "conda" ..!

--Thank you

dariober commented 3 years ago

Hi - I would suggest using conda

shivak3 commented 3 years ago

Hi Dariober,

I installed cnv_facets using conda as you said. After that, When I run cnv_facets.R I see the error with samtools -shared libraries

(cnv_facets) [test@rhel8 ]$ cnv_facets.R -t SR52.bam -n SR.bam -vcf ../../All.vcf.gz -o T23_HB72 
samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
samtools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
Error in if (n == 0) { : argument is of length zero
Calls: avg_insert_size
Execution halted

Please help to fix this issue. -- Thank you

dariober commented 3 years ago

Hi- samtools: error while loading shared libraries: libcrypto.so.1.0.0: is recurrent problem. Try to google it for more information and fixes. Can you show the commands you use to create the conda environment and install the dependencies along with their output?

shivak3 commented 3 years ago

Hi Dariober,

Thank you for your reply.

I followed the same steps you mentioned earlier to install conda environment.

conda create -n cnv_facets
conda activate cnv_facets
mamba install -c bioconda -c conda-forge cnv_facets

With the above environment, Samtools got installed version 1.7 and it caused the shared libraries error.

I upgraded samtools to 1.9 and it fixed the samtools error.

conda install -c bioconda samtools=1.9

-Thank you.

dariober commented 3 years ago

Thanks for reporting back. I'm going to close the issue then.