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rhysnewell / aviary

A hybrid assembly and MAG recovery pipeline (and more!)
GNU General Public License v3.0
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SyntaxWarning #169

Closed AroneyS closed 8 months ago

AroneyS commented 8 months ago

Getting some syntax warnings on running Aviary recover. Seems to run fine though... Due to python 3.12 update?

/mnt/hpccs01/home/aroneys/src/ibis/test/data/.conda/c5d58212560839c65fbe7671134d1bdc_/lib/python3.12/site-packages/aviary/modules/binning/binning.smk:1331: SyntaxWarning: invalid escape sequence '\;'
/mnt/hpccs01/home/aroneys/src/ibis/test/data/.conda/c5d58212560839c65fbe7671134d1bdc_/lib/python3.12/site-packages/aviary/modules/binning/binning.smk:1354: SyntaxWarning: invalid escape sequence '\;'
/mnt/hpccs01/home/aroneys/src/ibis/test/data/.conda/c5d58212560839c65fbe7671134d1bdc_/lib/python3.12/site-packages/aviary/modules/benchmarking/benchmarking.smk:161: SyntaxWarning: invalid escape sequence '\*'
  #         metabat2_cov = "data/metabat_bins_2/coverm.cov",
/mnt/hpccs01/home/aroneys/src/ibis/test/data/.conda/c5d58212560839c65fbe7671134d1bdc_/lib/python3.12/site-packages/aviary/modules/benchmarking/benchmarking.smk:171: SyntaxWarning: invalid escape sequence '\*'
  #         "../../envs/coverm.yaml"
/mnt/hpccs01/home/aroneys/src/ibis/test/data/.conda/c5d58212560839c65fbe7671134d1bdc_/lib/python3.12/site-packages/aviary/modules/benchmarking/benchmarking.smk:182: SyntaxWarning: invalid escape sequence '\*'
  # kmers = "data/rosella_bins/rosella_kmer_table.tsv"
/mnt/hpccs01/home/aroneys/src/ibis/test/data/.conda/c5d58212560839c65fbe7671134d1bdc_/lib/python3.12/site-packages/aviary/modules/benchmarking/benchmarking.smk:192: SyntaxWarning: invalid escape sequence '\*'
  max_contamination = 10,
/mnt/hpccs01/home/aroneys/src/ibis/test/data/.conda/c5d58212560839c65fbe7671134d1bdc_/lib/python3.12/site-packages/aviary/modules/benchmarking/benchmarking.smk:757: SyntaxWarning: invalid escape sequence '\;'
  # gsa_mappings = config["gsa_mappings"],
/mnt/hpccs01/home/aroneys/src/ibis/test/data/.conda/c5d58212560839c65fbe7671134d1bdc_/lib/python3.12/site-packages/aviary/modules/benchmarking/benchmarking.smk:781: SyntaxWarning: invalid escape sequence '\;'
  'data/amber_refine/*.tsv'
/mnt/hpccs01/home/aroneys/src/ibis/test/data/.conda/c5d58212560839c65fbe7671134d1bdc_/lib/python3.12/site-packages/aviary/modules/benchmarking/benchmarking.smk:1068: SyntaxWarning: invalid escape sequence '\;'
/mnt/hpccs01/home/aroneys/src/ibis/test/data/.conda/c5d58212560839c65fbe7671134d1bdc_/lib/python3.12/site-packages/aviary/modules/benchmarking/benchmarking.smk:1091: SyntaxWarning: invalid escape sequence '\;'
/mnt/hpccs01/home/aroneys/src/ibis/test/data/.conda/c5d58212560839c65fbe7671134d1bdc_/lib/python3.12/site-packages/aviary/modules/benchmarking/benchmarking.smk:1152: SyntaxWarning: invalid escape sequence '\;'
/mnt/hpccs01/home/aroneys/src/ibis/test/data/.conda/c5d58212560839c65fbe7671134d1bdc_/lib/python3.12/site-packages/aviary/modules/benchmarking/benchmarking.smk:1221: SyntaxWarning: invalid escape sequence '\;'
rhysnewell commented 8 months ago

I'd say this is a python3.12 related thing, those associated lines also don't seem to valid so I am not exactly sure which components of the snakemake files it is complaining about. We should limit python to be <=3.11 if the warnings are too verbose and can't be easily sorted