Installation issues - invalid escape sequence

[karenhn]

Hi, I'd like to use your package but I'm having issues with installation. I've followed all the steps until:

snakemake --use-conda --conda-create-envs-only --cores 1

But I get the following error messages:

/scratch/karenhn/KOunt/Snakefile:203: SyntaxWarning: invalid escape sequence '\/                                                     '
  filtered_gff=f'{outdir}Prodigal_Outputs/filtered_gffs/{{id}}/{{id}}.gff'
/scratch/karenhn/KOunt/Snakefile:219: SyntaxWarning: invalid escape sequence '\/                                                                  '
  rule bwa:
/scratch/karenhn/KOunt/Snakefile:680: SyntaxWarning: invalid escape sequence '\*                                                                  '
  touch {output}
/scratch/karenhn/KOunt/Snakefile:703: SyntaxWarning: invalid escape sequence '\*                                                                  '
  touch=f"{outdir}Touch/nohit_fa_{{id}}"
/scratch/karenhn/KOunt/Snakefile:748: SyntaxWarning: invalid escape sequence '\*                                                                  '
  '''
/scratch/karenhn/KOunt/Snakefile:767: SyntaxWarning: invalid escape sequence '\*                                                                  '
  of="6 qseqid sseqid pident qlen slen qstart qend sstart send evalue",
/scratch/karenhn/KOunt/Snakefile:807: SyntaxWarning: invalid escape sequence '\*                                                                  '
  raw=f"{outdir}diamond/NoHit_{{id}}_norna",
/scratch/karenhn/KOunt/Snakefile:825: SyntaxWarning: invalid escape sequence '\*                                                                  '
  shell:
FileNotFoundError in file /scratch/karenhn/KOunt/Snakefile, line 7:
[Errno 2] No such file or directory: 'test_fastqs/'
  File "/scratch/karenhn/KOunt/Snakefile", line 7, in <module>

I did try downloading the test_fastqs from the next step and rerunning the create envs code, but had the same issue. I'm fairly new to python etc, so could you tell me where I'm going wrong please?

[jmattock5]

Hi, thank you for your feedback. I think these warnings are occurring since a recent Snakemake update. I've updated the installation instructions in the README to specify the snakemake and mamba versions to install. Please could you try and make the snakemake_mamba env again and see if that solves the problem? Thanks, Jenny