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shenlab-sinai / ngsplot

Quick mining and visualization of NGS data by integrating genomic databases
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ngsplot error #68

Open amitpande74 opened 7 years ago

amitpande74 commented 7 years ago

Hi, ngsplot gives me an error Configuring variables...Error in CheckRegionAllowed(reg2plot, default.tbl) : Unknown region specified. Must be one of: bed Execution halted when I use -R flag with tss or genebody etc....but no errors when I specify my bed file. Can someone help.

clip78 commented 6 years ago

Adding a fix here to an old issue in case anyone else runs into it.

If you try to install a database and the ngsplotdb.py script is run using python3, it will error and not install completely. Then, when you run ngs.plot.r it cannot find tss in the database.

In the ngsplotdb.py and setTableDefaults.py files change the first line from

!/usr/bin/env python

to

!/usr/bin/env python2

This will ensure the scripts are run with py2.

deebhar commented 5 years ago

Hello

I have tried this solution but still I am getting the error when I am using tss or tes. Please suggest a solution.

aartrama commented 5 years ago

This error means that the genome's database is corrupted. Reinstall the database using ngsplotdb.py install ..., and make sure that all InstalledFeatures are present (cgi,exon,genebody,tss,tes) using 'ngsplotdb.py list' after installation.