ValueError: No closing quotation

[AceM1188]

Hi there,

I am trying to perform variant calling across four assembled bacterial genomes but have been running into problems on my new machine/OS. Specifically, pasnp (v2.1.2) has been installed via conda within it's own environment. This is being run on an Apple M3 Pro (MacOS Sequoia v15.2 (24C101)).

I've attached a compressed directory (support.zip) containing four fasta files, the gbk format version of the 0905 isolate which I have used as a reference using the -g flag (using the fasta-format of this isolate still results in the same aforementioned error), and the all_mumi.ini config file.
Of note, the output of the failed process generates the following stdout:

mherna17@DN2tf6pz ~/Library/CloudStorage/Box-Box/Matthew Hernandez's Externally Shareable Files/Lab/Aeromonas/NCBI-Annotated-Assemblies/variation
$ parsnp -g BIDMC_0905_CHR.gbk -d ./fasta/CHR/
Intel MKL WARNING: Support of Intel(R) Streaming SIMD Extensions 4.2 (Intel(R) SSE4.2) enabled only processors has been deprecated. Intel oneAPI Math Kernel Library 2025.0 will require Intel(R) Advanced Vector Extensions (Intel(R) AVX) instructions.
Intel MKL WARNING: Support of Intel(R) Streaming SIMD Extensions 4.2 (Intel(R) SSE4.2) enabled only processors has been deprecated. Intel oneAPI Math Kernel Library 2025.0 will require Intel(R) Advanced Vector Extensions (Intel(R) AVX) instructions.
15:53:02 - INFO - |--Parsnp 2.1.2--|

15:53:02 - INFO - 
****************************************************************************************************************************************************************************************
SETTINGS:
|-refgenome:	BIDMC_0905_CHR.gbk
|-genomes:	
	./fasta/CHR/BIDMC_0908_CHR.fasta
	./fasta/CHR/BIDMC_0905_CHR.fasta
	./fasta/CHR/BIDMC_0906_CHR.fasta
	./fasta/CHR/BIDMC_0907_CHR.fasta
|-aligner:	muscle
|-outdir:	/Users/mherna17/Library/CloudStorage/Box-Box/Matthew Hernandez's Externally Shareable Files/Lab/Aeromonas/NCBI-Annotated-Assemblies/variation/P_2025_01_13_155302524412
|-OS:	Darwin
|-threads:	1
****************************************************************************************************************************************************************************************
    
15:53:02 - INFO - <<Parsnp started>>
15:53:02 - INFO - Filtering genomes...
Traceback (most recent call last):
  File "/Users/mherna17/micromamba/envs/parsnip/bin/parsnp", line 1367, in <module>
    run_logged_command(command=command, outputDir=outputDir, label="parsnp-mumi")
  File "/Users/mherna17/micromamba/envs/parsnip/bin/parsnp", line 256, in run_logged_command
    return run_command(command=command, stdout=stdout_f, stderr=stderr_f, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mherna17/micromamba/envs/parsnip/bin/parsnp", line 261, in run_command
    result = subprocess.run(shlex.split(command), stderr=stderr, stdout=stdout)
                            ^^^^^^^^^^^^^^^^^^^^
  File "/Users/mherna17/micromamba/envs/parsnip/lib/python3.12/shlex.py", line 313, in split
    return list(lex)
           ^^^^^^^^^
  File "/Users/mherna17/micromamba/envs/parsnip/lib/python3.12/shlex.py", line 300, in __next__
    token = self.get_token()
            ^^^^^^^^^^^^^^^^
  File "/Users/mherna17/micromamba/envs/parsnip/lib/python3.12/shlex.py", line 109, in get_token
    raw = self.read_token()
          ^^^^^^^^^^^^^^^^^
  File "/Users/mherna17/micromamba/envs/parsnip/lib/python3.12/shlex.py", line 191, in read_token
    raise ValueError("No closing quotation")
ValueError: No closing quotation

Any advice would be helpful for how best to address this.

Thanks in advance.

[bkille]

Hi @AceM1188, thanks for opening an issue and attaching the files!

I am able to run parsnp on these files with no issue. Due to the error message you received and the path the files are located at, my guess is that it is due to the name of this directory containing a single quote '`'

Matthew Hernandez's Externally Shareable Files

Having a single or double quote in the filename can confuse the shell/terminal. Please let me know if the issue persists!

-Bryce