zahidul-islam-nahid
commented
3 months ago The issue is resolved. I have to omit the option -b which is for blasting new alleles to find the closest one.
Closed zahidul-islam-nahid closed 2 months ago
zahidul-islam-nahid
commented
3 months ago The issue is resolved. I have to omit the option -b which is for blasting new alleles to find the closest one.
zahidul-islam-nahid
commented
3 months ago I am also getting error for trying to get the genogroup of NG-MAST
pyngoST.py -i contigs/------.fasta -s NG-STAR,MLST,NG-MAST -g -o output_------ -t 16 -p /____/tools/pyngost/allelesDB/
Traceback (most recent call last):
File "/home/nahid/tools/pyngost/lib/python3.11/site-packages/pyngoST/pyngoST.py", line 142, in
leosanbu
commented
2 months ago Hi, regarding your first comment: I have now updated pyngoST so it does not crash when trying to report mosaic penAs from novel alleles with a, i.e. '2.002-1', structure. It will see that 2.002 is a NonMosaic and report it as 'NonMosaic-like'.
leosanbu
commented
2 months ago On your second comment, i am not sure what the problem is, it works for me with test dataset. Do you have a working installation of 'muscle'?
Jolein-Laumen
commented
1 month ago Hi Leonor and Zahidul,
I got the same error when including the -g argument: _Bio.Application.ApplicationError: Non-zero return code 1 from 'muscle -in POR_out.fas -out POR_out.aln', message 'Invalid command line'
I found out this was caused because the newer muscle version I installed (5.1) uses the arguments -align and -output instead of -in and -out used in the current pyngoST script. The problem is solved by installing muscle version 3.8.1551. Maybe you could add a paragraph on the dependent packages and their versions (muscle==3.8.1551 and blast), or adapt the arguments in the script.
In addition, adding the -q argument to indicate the path used to save output files prevents the alignment of POR_out.fas and TBPB_out.fas and as a result does not save a report or print the table to the screen
I have run 24 N. gonorrhoeae sequences and getting the following error.
pyngoST.py -r fastafiles -s NG-STAR,MLST,NG-MAST -g -m -b -a -o output -t 16 -p /home____/pyngost/allelesDB/
pyngoST: multiple sequence typing of Neisseria gonorrhoeae for large assembly collections
Loading databases...
Schemes requested: NG-STAR,MLST,NG-MAST,NG-MAST Genogroups
Number of processes: 16
Finding matches...
Traceback (most recent call last): File "/home/nahid/tools/pyngost/lib/python3.11/site-packages/pyngoST/pyngoST.py", line 139, in
finalresults, ngmastClusters = access_results(results, genogroups)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/nahid/tools/pyngost/lib/python3.11/site-packages/pyngoST/pyngoST_utils.py", line 750, in access_results
for f, all_results in results:
File "/home/nahid/anaconda3/lib/python3.11/concurrent/futures/_base.py", line 619, in result_iterator
yield _result_or_cancel(fs.pop())
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/nahid/anaconda3/lib/python3.11/concurrent/futures/_base.py", line 317, in _result_or_cancel
return fut.result(timeout)
^^^^^^^^^^^^^^^^^^^
File "/home/nahid/anaconda3/lib/python3.11/concurrent/futures/_base.py", line 449, in result
return self.get_result()
^^^^^^^^^^^^^^^^^^^
File "/home/nahid/anaconda3/lib/python3.11/concurrent/futures/_base.py", line 401, in get_result
raise self._exception
File "/home/nahid/anaconda3/lib/python3.11/concurrent/futures/thread.py", line 58, in run
result = self.fn(*self.args, **self.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/nahid/tools/pyngost/lib/python3.11/site-packages/pyngoST/pyngoST_utils.py", line 737, in process_files
st_list['NG-STAR'] += '\t'+penAmosaicsdic[penA]