ModuleNotFoundError: No module named 'ext_tools.Flye.flye.six.moves'

[novigit]

I'm on MacOS Ventura, and I installed Tandemtools as follows

First I cloned the github repo

git clone [email protected]:ablab/TandemTools.git

then I installed the dependencies in a new conda environment with

mamba create -n tandemtools --file requirements.txt

I'm able to succesfully invoke tandemmapper after activating the tandemtools environment with

~/tools/TandemTools/tandemmapper.py --help

However, when I try to actually do some mapping with

~/tools/TandemTools/tandemmapper.py --nano eb_flongle_reads_pooled.fastq.gz -o test_out -t4 canu_ergo_contigs.fasta

I'm running into the following error:

2024-04-30 15:40:55 TandemMapper started
/Users/joran/tools/TandemTools/scripts/select_kmers.py:30: SyntaxWarning: invalid escape sequence '\i'
  make_plot(plot_fname, "Distribution of %s k-mers" % kmers_type, label, xlabel="Position", ylabel="$\it{k}$-mer counts",
/Users/joran/tools/TandemTools/scripts/select_kmers.py:96: SyntaxWarning: invalid escape sequence '\d'
  version_pattern = re.compile('(?P<major_version>\d+)\.(?P<minor_version>\d+)')
/Users/joran/tools/TandemTools/scripts/select_kmers.py:177: SyntaxWarning: invalid escape sequence '\i'
  make_plot(plot_fname, "Histogram of k-mer occurrences", assembly.label, xlabel="Occurrences in reads", ylabel="$\it{k}$-mer counts",
Traceback (most recent call last):
  File "/Users/joran/tools/TandemTools/tandemmapper.py", line 80, in <module>
    main()
  File "/Users/joran/miniconda3/envs/tandemtools/lib/python3.12/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/joran/miniconda3/envs/tandemtools/lib/python3.12/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/Users/joran/miniconda3/envs/tandemtools/lib/python3.12/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/joran/miniconda3/envs/tandemtools/lib/python3.12/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/joran/tools/TandemTools/tandemmapper.py", line 45, in main
    from scripts import select_kmers, make_alignments
  File "/Users/joran/tools/TandemTools/scripts/make_alignments.py", line 11, in <module>
    from ext_tools.Flye.flye.polishing.polish import ASSEMBLY_BIN
  File "/Users/joran/tools/TandemTools/ext_tools/Flye/flye/polishing/polish.py", line 18, in <module>
    from ext_tools.Flye.flye.polishing.alignment import (make_alignment, get_contigs_info,
  File "/Users/joran/tools/TandemTools/ext_tools/Flye/flye/polishing/alignment.py", line 18, in <module>
    from ext_tools.Flye.flye.utils.sam_parser import AlignmentException, preprocess_sam
  File "/Users/joran/tools/TandemTools/ext_tools/Flye/flye/utils/sam_parser.py", line 24, in <module>
    from ext_tools.Flye.flye.six.moves import range
ModuleNotFoundError: No module named 'ext_tools.Flye.flye.six.moves'