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Question: COHCAP Perl error while running commands
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gravatar for poojitha.stemcell
9 months ago by
poojitha.stemcell0 wrote:

I am using COHCAP for the first time to correlate DNA methylation and gene expression data. I have been getting an error message (highlighted text below) regarding Perl not being found.

filtered.sites = COHCAP.site(sample.file, beta.table, project.name,project.folder, ref="Control")
"Reading Sample Description File...."
6768    8
6768    8
"Differential Methylation Stats for 2 Groups with Reference"
6768    5
[6768   10

The Perl script 'WriteXLSX.pl' failed to run successfully.
Error in system(cmd, intern = TRUE, wait = TRUE) : 'perl' not found
In addition: Warning message:
running command 'perl -I"C:/Users/mszpr2/Documents/R/win-library/3.3/WriteXLS/Perl" "C:/Users/mszpr2/Documents/R/win-library/3.3/WriteXLS/Perl/WriteXLSX.pl" --CSVPath "C:\Users\mszpr2\AppData\Local\Temp\Rtmpa0dyB1/WriteXLS" --verbose FALSE --AdjWidth FALSE --AutoFilter FALSE --BoldHeaderRow FALSE --FreezeRow 0 --FreezeCol 0 --Encoding UTF-8 "C:\Users\mszpr2\Desktop\thesis\DNA meth data analysis\COHCAP-correlating meth and exp\Raw_Data\methVsexp_CpG_site_stats.xlsx"' had status 127

I have tried several solutions suggested online such as (i) reinstalling updated version of COHCAP (ii) installing strawberry perl and updating gdata and COHCAP packages (iii) tried resetting the path of wig files:

cmd<-'Perl C:/Users/mszpr2/Documents/R/win-library/3.3/COHCAP/Perl/create_wig_files.pl'

system(cmd, intern=TRUE, wait=TRUE)
Error in system(cmd, intern = TRUE, wait = TRUE) : 'perl' not found

Could anyone help me resolve this problem with Perl?

Thank you.

Regards,

Poojitha

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