Pipeline dies at building database

[kguynes]

Hi,

Many thanks for creating a wonderful tool. Unfortunately, I have attempted to run this pipeline several times using the genomic fasta file I acquired from https://parasite.wormbase.org/Caenorhabditis_angaria_prjna51225/Info/Index but to no avail.

I'll copy the error messages here for clarity:

	<<< Cleaning Genome >>>
Traceback (most recent call last):
  File "/usr/local/share/earlgrey-5.0.0-0/scripts//faswap.py", line 11, in <module>
    a=dict(csv.reader(open(dictionary),delimiter="\t"))
  File "/usr/local/lib/python3.9/codecs.py", line 322, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x94 in position 3: invalid start byte
    
              )  (
	     (   ) )
	     ) ( (
	   _______)_
	.-'---------|  
       ( C|/\/\/\/\/|
	'-./\/\/\/\/|
	 '_________'
	  '-------'
	<<< Detecting Novel Repeats >>>
Building database cAngaria:
  Reading /users/xx/00-Reference_genomes/00-C.angaria/caenorhabditis_angaria.PRJNA51225.WBPS19.genomic.fa.gz.prep...
Died at /usr/local/bin/BuildDatabase line 331.
The makeblastdb program exited with code 1.  Please check your input file(s) for potential formating errors.
/usr/local/bin/makeblastdb returned: 

I ran the RepeatModeler tool to build database and compute TE annotation to test if this is indeed an issue with the fasta file, but it seems to run without an issue.

Not sure how to mitigate the issue I'm running into with the EarlGrey tool. Any help/pointers would be greatly appreciated.

Thank you very much in advance!