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shenlab-sinai / ngsplot

Quick mining and visualization of NGS data by integrating genomic databases
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Issue with Tair10 Genome #96

Closed jjp55 closed 1 year ago

jjp55 commented 2 years ago

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.