runChicago.R error | designing-directory not parsing

Issue #59 new
Anupam Bhattacharya created an issue

Hi,
Currently, I am exploring Chicago tool with the GM12878 datasets(downloaded from https://osf.io/nemc6/files/.))

I am experiencing an error while running runChicago.R script.

Rscript runChicago.R --design-dir /storage2/bif_works/chicago_tool/chicago/chicagoTools/designDir/ GM12878_chinput/GM12878_rep1_549.chinput Gm12878.out

error:
[bif@spandana chicagoTools]$ Rscript runChicago.R GM12878_chinput/GM12878_rep1_549.chinput Gm12878.out

***runChicago.R

Loading the Chicago package and dependencies...
Loading required package: data.table
Welcome to CHiCAGO - version 1.10.1
If you are new to CHiCAGO, please consider reading the vignette through the command: vignette("Chicago").
NOTE: Default values of tlb.minProxOEPerBin and tlb.minProxB2BPerBin changed as of Version 1.1.5. No action is required unless you specified non-default values, or wish to re-run the pipeline on old chicagoData objects. See news(package="Chicago")
Warning: neither --en-feat-files nor --en-feat-list provided. Feature enrichments will not be computed

Setting the experiment...

Error in setExperiment(designDir = designDir, settingsFile = settingsFile) :
** Design not specified. Please specify a design directory or design files.
Execution halted**

I have used the HindIII design files(hg19) from your server.

The design directory contains the necessary files as per the manual.

Human_HindIII_NBaitsPerBin.nbpb
Human_HindIII_proxOE.poe
Human_HindIII_NperBin.npb
Digest_Human_HindIII.rmap
Digest_Human_HindIII_baits_e75_ID.baitmap
Digest_Human_HindIII_baits_e75_ID.baitmap_4col.txt

I am using R version 3.5.1

Any help would be appreciated.

Regards;
Anupam

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