how to run FacetsSuite wrapper scripts on command line

Question

[Dalal]

Hi,

I am very new to using FACETS. I was wondering if there is a way to run the Rscript snp-pile-wrapper.R directly on the command line without installing facets using conda or from GitHub. Is this possible? I've tried running this using the following example command provided at https://github.com/mskcc/facets-suite#, substituting the arguments with the actual paths to my files and chosen prefixes:

snp-pileup-wrapper.R \
    --snp-pileup-path <path to snp-pileup executable> \
    --vcf-file <path to SNP VCF> \
    --normal-bam normal.bam \
    --tumor-bam tumor.bam \
    --output-prefix <prefix for output file, preferrably tumorSample__normalSample>

However, I get the following error:

'snp-pileup-wrapper.R: command not found'

The Rscript is located within the path supplied after --snp-pileup-path.

[GenoMax]

Do you have R installed (and argparse library)?

Rscript --vanilla your_command_line

[Dalal]

Thanks for your response. Yes I have R and argparse package installed.

Using your suggested command outputs the error:

'sh: 1: /home/dalal/mut_analysis/variant-calling/facets_cnv/: Permission denied'

I have write and execute permissions to this directory.

[GenoMax]

Your command line must have an incorrect option. Can you provide your command line (obfuscate any real names if you want).

[Dalal]

This is the code I ran:

Rscript --vanilla snp-pileup-wrapper.R --snp-pileup-path ~/mut_analysis/variant-calling/facets_cnv/ --vcf-file ~/mut_analysis/hg38/annotations/dbsnp_146.hg38.vcf.gz --normal-bam ~/bam/006_normal/006_normal.clean.bam --tumor-bam ~/bam/006_met/006_met.clean.bam --output-prefix 006_met__006_normal

Answer 1

[dariober]

snp-pileup-wrapper.R: command not found

Have you put snp-pileup-wrapper.R in a directory on your PATH and, just in case, make it executable first with

chmod a+x snp-pileup-wrapper.R

If it is not on your PATH, then you need either

./snp-pileup-wrapper.R --foo --bar ...

(note ./) if the script is in your current directory. Or use the full path:

/full/path/to/snp-pileup-wrapper.R --foo --bar ...

---

As an aside, a while back I happen to write a wrapper for snp-pileup and facets. If any useful, it's on github cnv_facets.

[Dalal]

Hello, thanks for your reply and for kindly directing me to your GitHub page. Unfortunately I've tried installing cnv_facets via conda prior to this and it has taken a very long time at solving environment.

snp-pileup-wrapper.R is in my current directory. I've also ensured that the script is executable:

chmod a+x snp-pileup-wrapper.R

./snp-pileup-wrapper.R --foo --bar --snp-pileup-path ~/mut_analysis/variant-calling/facets_cnv/ --vcf-file ~/mut_analysis/hg38/annotations/dbsnp_146.hg38.vcf.gz --normal-bam ~/bam/006_normal/006_normal.clean.bam --tumor-bam ~/bam/006_met/006_met.clean.bam --output-prefix 006_met__006_normal

usage: ./snp-pileup-wrapper.R [-h] [-v] [-sp SNP_PILEUP_PATH] -vcf VCF_FILE -n NORMAL_BAM -t TUMOR_BAM -o OUTPUT_PREFIX [-p PSEUDO_SNPS] [-d MAX_DEPTH] ./snp-pileup-wrapper.R: error: unrecognized arguments: --foo --bar

I am probably inputting the incorrect commands at this point.

[GenoMax]

You need to replace -foo --bar with real options for the script. Those dummy names were just a demonstration of how you will provide those options.

[Dalal]

I apologise for that. Unfortunately I am still left with the same error:

sh: 1: ~/mut_analysis/variant-calling/facets_cnv/: Permission denied

[GenoMax]

The link in your original post has this bit of help

--snp-pileup-path <path to snp-pileup executable>

So the path you provide needs to contain this executable. Do you have that in that directory?

[Dalal]

Yes, the executable snp-pileup-wrapper.R is found in the path directory provided.

pwd

/home/dalal/mut_analysis/variant-calling/facets_cnv

ls -ltrh

total 28K -rw-rw-r-- 1 dalal dalal 15K May 24 19:59 run-facets-wrapper.R -rw-rw-r-- 1 dalal dalal 5.2K May 24 20:00 annotate-maf-wrapper.R -rwxrwxr-x 1 dalal dalal 2.3K May 24 20:47 snp-pileup-wrapper.R

[GenoMax]

Unfortunately the vignette is not very clear. It appears that you need to compile a program called snp-pileup and have it available in the directory that you are providing above.

Instructions to do the compilation are buried in the extcode directory from the facets program bundle: https://github.com/mskcc/facets/tree/master/inst/extcode

Please check the readme.txt file there.