makedb from gbk files

[Tim-Kirkwood]

Hello, I am trying to make a database from some genbank files. They were downloaded using these links, clicking on the 'Download' tab then 'Download Genbank summary file':

https://mibig.secondarymetabolites.org/repository/BGC0000001/index.html#r1c1 https://mibig.secondarymetabolites.org/repository/BGC0001694/index.html#r1c1 https://mibig.secondarymetabolites.org/repository/BGC0001492/index.html#r1c1

I have run across the following issue (I get the same issue when I use a full filepath for mydb and just '-n mydb' alone):

cblaster makedb "path\to\test_db\BGC0000001.gbk" "path\to\test_db\BGC0001492.gbk" "path\to\test_db\BGC0001694.gbk" -n "path\to\test_db\mydb" Importing genomicsqlite failed, falling back to SQLite3 [10:46:33] INFO - Starting makedb module [10:46:33] INFO - Pre-existing files found, overwriting [10:46:33] INFO - Overwriting pre-existing file at mydb.sqlite3 [10:46:33] INFO - Parsing 3 genome files, in 1 batches of 3 [10:46:33] INFO - Processing batch 1 [10:46:33] INFO - BGC0000001.gbk [10:46:33] INFO - BGC0001492.gbk [10:46:33] INFO - BGC0001694.gbk [10:46:33] INFO - Saving 95 genes [10:46:34] INFO - Writing FASTA to mydb.fasta [10:46:34] INFO - Building DIAMOND database at mydb.dmnd 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 File "c:\anaconda3\lib\site-packages\cblaster\main.py", line 428, in main force=args.force, File "c:\anaconda3\lib\site-packages\cblaster\database.py", line 239, in makedb diamond_makedb(fasta_path, dmnd_path, cpus) File "c:\anaconda3\lib\site-packages\cblaster\database.py", line 144, in diamond_makedb stderr=subprocess.DEVNULL, File "c:\anaconda3\lib\subprocess.py", line 472, in run with Popen(*popenargs, **kwargs) as process: File "c:\anaconda3\lib\subprocess.py", line 775, in init restore_signals, start_new_session) File "c:\anaconda3\lib\subprocess.py", line 1119, in _execute_child args = list2cmdline(args) File "c:\anaconda3\lib\subprocess.py", line 530, in list2cmdline needquote = (" " in arg) or ("\t" in arg) or not arg TypeError: argument of type 'WindowsPath' is not iterable

Do you have any suggestions on how to fix this? I am windows 10, and should be working with the latest cblaster version (I uninstalled and reinstalled it with pip whilst I installed diamond for local searching)

Many thanks!