Thank you for making this excellent tool. Using windows 10 and the BGC0001742_pieA1_A6.fasta query, I ran COMMAND and got the following command line READOUT. It seems to have an issue parsing the hits (error is at the bottom of the command line readout.
Importing genomicsqlite failed, falling back to SQLite3
[12:23:44] INFO - Starting cblaster in remote mode
[12:23:44] INFO - Launching new search
[12:23:48] INFO - Request Identifier (RID): ZV0EJNX4013
[12:23:48] INFO - Request Time Of Execution (RTOE): 34s
[12:24:22] INFO - Polling NCBI for completion status
[12:24:22] INFO - Checking search status...
[12:25:22] INFO - Checking search status...
[12:26:22] INFO - Checking search status...
[12:27:22] INFO - Checking search status...
[12:28:22] INFO - Checking search status...
[12:29:22] INFO - Checking search status...
[12:30:22] INFO - Checking search status...
[12:31:22] INFO - Checking search status...
[12:32:22] INFO - Checking search status...
[12:33:22] INFO - Checking search status...
[12:33:23] INFO - Search has completed successfully!
[12:33:23] INFO - Retrieving results for search ZV0EJNX4013
[12:38:13] INFO - Parsing results...
[12:38:13] INFO - Found 43834 hits meeting score thresholds for remote search
[12:38:13] INFO - Fetching genomic context of hits
Traceback (most recent call last):
File "c:\anaconda3\lib\runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "c:\anaconda3\lib\runpy.py", line 85, in _run_code
exec(code, run_globals)
File "C:\ANACONDA3\Scripts\cblaster.exe\__main__.py", line 9, in <module>
File "c:\anaconda3\lib\site-packages\cblaster\main.py", line 473, in main
dmnd_sensitivity=args.dmnd_sensitivity,
File "c:\anaconda3\lib\site-packages\cblaster\main.py", line 342, in cblaster
percentage=percentage,
File "c:\anaconda3\lib\site-packages\cblaster\context.py", line 595, in search
organisms = parse_IPG_table(rows, hits)
File "c:\anaconda3\lib\site-packages\cblaster\context.py", line 205, in parse_IPG_table
groups = parse_IP_groups(results)
File "c:\anaconda3\lib\site-packages\cblaster\context.py", line 142, in parse_IP_groups
entry = Entry(*fields)
TypeError: __new__() missing 8 required positional arguments: 'start', 'end', 'strand', 'protein_id', 'protein_name', 'organism', 'strain', and 'assembly'
Hello,
Thank you for making this excellent tool. Using windows 10 and the BGC0001742_pieA1_A6.fasta query, I ran COMMAND and got the following command line READOUT. It seems to have an issue parsing the hits (error is at the bottom of the command line readout.
Any suggestions on how to fix this?
Many thanks!
COMMAND: cblaster search -qf "C:/Users/u03132tk/.spyder-py3/piericidin A1/BGC0001742_pieA1_A6.fasta" -o "C:/Users/u03132tk/.spyder-py3/piericidin A1/BGC0001742_summary.csv" -ode "," -p "C:/Users/u03132tk/.spyder-py3/piericidin A1/BGC0001742_plot.html" -b "C:/Users/u03132tk/.spyder-py3/piericidin A1/BGC0001742_binary.csv" -bde "," -s "C:/Users/u03132tk/.spyder-py3/piericidin A1/BGC0001742_session.json"
READOUT:
BGC0001742_pieA1_A6.fasta: