shenlab-sinai/ngsplot

Issue with Tair10 Genome

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jjp55 commented

Hello,

I seem to be having some issues with the Tair10 genome.

When I was running the command:
ngs.plot.r -G Tair10 -R genebody -C MNase_config_clusters.txt -O MNase_test
I got back the following error:

Configuring variables...Error in CheckRegionAllowed(reg2plot, default.tbl) : 
Unknown region specified. Must be one of: bed 
Execution halted

I checked to make sure Tair10 was installed using:
jp-MBP: Desktop jp$ ngsplotdb.py list
And it returned:

ID       Assembly Species              EnsVer   NPVer    InstalledFeatures    
Tair10   TAIR10   arabidopsis_thaliana 21.0     3.0                        

I tried to remove and reinstall it, but I went to remove it I got the error:

Removing genome...
Traceback (most recent call last):
  File "/Users/jp/opt/anaconda3/envs/ngsplot/bin/ngsplotdb.py", line 669, in <module>
    args.func(root_path, args)
  File "/Users/jp/opt/anaconda3/envs/ngsplot/bin/ngsplotdb.py", line 528, in remove
    shutil.rmtree(folder_to_rm)
  File "/Users/jp/opt/anaconda3/envs/ngsplot/lib/python2.7/shutil.py", line 253, in rmtree
    onerror(os.listdir, path, sys.exc_info())
  File "/Users/jp/opt/anaconda3/envs/ngsplot/lib/python2.7/shutil.py", line 251, in rmtree
    names = os.listdir(path)
OSError: [Errno 2] No such file or directory: '/Users/jp/opt/anaconda3/envs/ngsplot/share/r-ngsplot-2.63-7/database/Tair10

Any help would be greatly appreciated.