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transPACT - trans-AT PKS Annotation and Comparison Tool
GNU Affero General Public License v3.0
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Problem when generating the dendrogram #2

Open Rafael12692 opened 3 years ago

Rafael12692 commented 3 years ago

Hi,

The first command line is working fine here, but I can't get the dendrogram line to work. Could you please help me? I couldn't find any solution on my own (my background is not in computer science).

(transPACTtest) XXXX@XXXX-server:~/transPACT$ ls antismash conda_packages.txt data example images KSs.faa LICENSE mags README.md transPACT_substrate_from_faa.py (transPACTtest) XXXX@XXXX-server:~/transPACT$ /usr/bin/python2 transPACT_substrate_from_faa.py KSs.faa 1 Clade_8 GNAT_Starter 2 Clade_12 reduced/shifted_double_bonds 3 Clade_12 reduced/shifted_double_bonds 4 Clade_11 oxygen_insertion 5 Clade_113 a_Me_b_OH 6 Clade_82 b_MeeDB 7 Clade_3 bimod_bOH 8 Clade_69 zDB 9 clade_not_conserved NA 10 Clade_62 eDB 11 Clade_113 a_Me_b_OH 12 Clade_87 exometh/red_bMe 13 Clade_75 non_elongating_oxazole/thiazole 14 Clade_44 oxazole/thiazole 15 Clade_62 eDB (transPACTtest) XXXX@XXXX-server:~/transPACT$ ls aligned.fasta antismash conda_packages.txt data example images KSs.faa LICENSE mags README.md transPACT_substrate_from_faa.py (transPACTtest) XXXX@XXXX-server:~/transPACT$ /usr/bin/python2 data/dendrogram20190829/generate_dendrogram_userweights.py 0 0.32 0.68 /usr/local/lib/python2.7/dist-packages/pkg_resources/py2_warn.py:21: UserWarning: Setuptools will stop working on Python 2

You are running Setuptools on Python 2, which is no longer supported and

SETUPTOOLS WILL STOP WORKING <<< in a subsequent release (no sooner than 2020-04-20). Please ensure you are installing Setuptools using pip 9.x or later or pin to setuptools<45 in your environment. If you have done those things and are still encountering this message, please follow up at https://bit.ly/setuptools-py2-warning.

sys.version_info < (3,) and warnings.warn(pre + "" 60 + msg + "" 60) Traceback (most recent call last): File "data/dendrogram20190829/generate_dendrogram_userweights.py", line 572, in Jaccardw, GKw, DDSw, AIw = float(sys.argv[1]), float(sys.argv[2]), float(sys.argv[3]), float(sys.argv[4]) IndexError: list index out of range

mathijs-m commented 2 years ago

There seems to be a missing command line argument that is not documented. You need to add a value for all four variables in line 572. So if you run /transPACT$ /usr/bin/python2 data/dendrogram20190829/generate_dendrogram_userweights.py 0 0 0.32 0.68, the code advances.