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  • Problem with orthofinder and dlacpar

    Hi there,
    Hope this mail will find you in sound. I was trying to install dlcpar in my linux workstation. I failed everytime. I was trying in many ways but still no luck. Here are the error messages:
    Code:
    [zillur@genomics dlcpar-master]$ python setup.py install --home=~
    running install
    running build
    running build_py
    running build_scripts
    running install_lib
    creating /home/zillur/lib
    creating /home/zillur/lib/python
    creating /home/zillur/lib/python/dlcpar
    copying build/lib/dlcpar/__init__.py -> /home/zillur/lib/python/dlcpar
    copying build/lib/dlcpar/common.py -> /home/zillur/lib/python/dlcpar
    copying build/lib/dlcpar/countvector.py -> /home/zillur/lib/python/dlcpar
    copying build/lib/dlcpar/recon.py -> /home/zillur/lib/python/dlcpar
    copying build/lib/dlcpar/reconlib.py -> /home/zillur/lib/python/dlcpar
    copying build/lib/dlcpar/reconscape.py -> /home/zillur/lib/python/dlcpar
    copying build/lib/dlcpar/simplerecon.py -> /home/zillur/lib/python/dlcpar
    creating /home/zillur/lib/python/dlcpar/deps
    creating /home/zillur/lib/python/dlcpar/deps/rasmus
    copying build/lib/dlcpar/deps/rasmus/__init__.py -> /home/zillur/lib/python/dlcpar/deps/rasmus
    copying build/lib/dlcpar/deps/rasmus/linked_list.py -> /home/zillur/lib/python/dlcpar/deps/rasmus
    copying build/lib/dlcpar/deps/rasmus/plotting.py -> /home/zillur/lib/python/dlcpar/deps/rasmus
    copying build/lib/dlcpar/deps/rasmus/stats.py -> /home/zillur/lib/python/dlcpar/deps/rasmus
    copying build/lib/dlcpar/deps/rasmus/tablelib.py -> /home/zillur/lib/python/dlcpar/deps/rasmus
    copying build/lib/dlcpar/deps/rasmus/textdraw.py -> /home/zillur/lib/python/dlcpar/deps/rasmus
    copying build/lib/dlcpar/deps/rasmus/timer.py -> /home/zillur/lib/python/dlcpar/deps/rasmus
    copying build/lib/dlcpar/deps/rasmus/treelib.py -> /home/zillur/lib/python/dlcpar/deps/rasmus
    copying build/lib/dlcpar/deps/rasmus/util.py -> /home/zillur/lib/python/dlcpar/deps/rasmus
    creating /home/zillur/lib/python/dlcpar/deps/compbio
    copying build/lib/dlcpar/deps/compbio/__init__.py -> /home/zillur/lib/python/dlcpar/deps/compbio
    copying build/lib/dlcpar/deps/compbio/birthdeath.py -> /home/zillur/lib/python/dlcpar/deps/compbio
    copying build/lib/dlcpar/deps/compbio/coal.py -> /home/zillur/lib/python/dlcpar/deps/compbio
    copying build/lib/dlcpar/deps/compbio/fasta.py -> /home/zillur/lib/python/dlcpar/deps/compbio
    copying build/lib/dlcpar/deps/compbio/phylo.py -> /home/zillur/lib/python/dlcpar/deps/compbio
    copying build/lib/dlcpar/deps/compbio/phyloDLC.py -> /home/zillur/lib/python/dlcpar/deps/compbio
    copying build/lib/dlcpar/deps/compbio/seqlib.py -> /home/zillur/lib/python/dlcpar/deps/compbio
    byte-compiling /home/zillur/lib/python/dlcpar/__init__.py to __init__.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/common.py to common.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/countvector.py to countvector.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/recon.py to recon.cpython-35.pyc
      File "/home/zillur/lib/python/dlcpar/recon.py", line 213
        subtrees_snode.sort(key=lambda (root, rootchild, leaves): ids[root.name])
                                       ^
    SyntaxError: invalid syntax
    
    byte-compiling /home/zillur/lib/python/dlcpar/reconlib.py to reconlib.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/reconscape.py to reconscape.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/simplerecon.py to simplerecon.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/__init__.py to __init__.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/linked_list.py to linked_list.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/plotting.py to plotting.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/stats.py to stats.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/tablelib.py to tablelib.cpython-35.pyc
      File "/home/zillur/lib/python/dlcpar/deps/rasmus/tablelib.py", line 353
        except Exception, e:
                        ^
    SyntaxError: invalid syntax
    
    byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/textdraw.py to textdraw.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/timer.py to timer.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/treelib.py to treelib.cpython-35.pyc
      File "/home/zillur/lib/python/dlcpar/deps/rasmus/treelib.py", line 1088
        print i, parentid
              ^
    SyntaxError: Missing parentheses in call to 'print'
    
    byte-compiling /home/zillur/lib/python/dlcpar/deps/rasmus/util.py to util.cpython-35.pyc
      File "/home/zillur/lib/python/dlcpar/deps/rasmus/util.py", line 114
        print str(j) + ", ",
                ^
    SyntaxError: invalid syntax
    
    byte-compiling /home/zillur/lib/python/dlcpar/deps/compbio/__init__.py to __init__.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/deps/compbio/birthdeath.py to birthdeath.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/deps/compbio/coal.py to coal.cpython-35.pyc
      File "/home/zillur/lib/python/dlcpar/deps/compbio/coal.py", line 1608
        print p, N, t
              ^
    SyntaxError: Missing parentheses in call to 'print'
    
    byte-compiling /home/zillur/lib/python/dlcpar/deps/compbio/fasta.py to fasta.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/deps/compbio/phylo.py to phylo.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/deps/compbio/phyloDLC.py to phyloDLC.cpython-35.pyc
    byte-compiling /home/zillur/lib/python/dlcpar/deps/compbio/seqlib.py to seqlib.cpython-35.pyc
    running install_scripts
    creating /home/zillur/bin
    copying build/scripts-3.5/dlcpar -> /home/zillur/bin
    copying build/scripts-3.5/dlcpar_search -> /home/zillur/bin
    copying build/scripts-3.5/dlcoal_to_dlcpar -> /home/zillur/bin
    copying build/scripts-3.5/dlcpar_to_dlcoal -> /home/zillur/bin
    copying build/scripts-3.5/tree-events-dlc -> /home/zillur/bin
    copying build/scripts-3.5/tree-events-dlcpar -> /home/zillur/bin
    changing mode of /home/zillur/bin/dlcpar to 775
    changing mode of /home/zillur/bin/dlcpar_search to 775
    changing mode of /home/zillur/bin/dlcoal_to_dlcpar to 775
    changing mode of /home/zillur/bin/dlcpar_to_dlcoal to 775
    changing mode of /home/zillur/bin/tree-events-dlc to 775
    changing mode of /home/zillur/bin/tree-events-dlcpar to 775
    running install_egg_info
    Writing /home/zillur/lib/python/dlcpar-1.0.1-py3.5.egg-info
    But,
    Code:
    [zillur@genomics dlcpar-master]$ cd /home/zillur/bin/
    [zillur@genomics bin]$ ls
    dlcoal_to_dlcpar  dlcpar  dlcpar_search  dlcpar_to_dlcoal  tree-events-dlc  tree-events-dlcpar
    [zillur@genomics bin]$ ./dlcpar
    Traceback (most recent call last):
      File "./dlcpar", line 10, in <module>
        import dlcpar
    ImportError: No module named 'dlcpar'"
    When I tried to run orthofinder, it works fine, finding all the dependencies but not dlcpar.
    Code:
    Test can run "fastme -i /home/zillur/Desktop/zillur/phd/orthofinder/fasta/test/Results_Nov23/WorkingDirectory/SimpleTest.phy -o /home/zillur/Desktop/zillur/phd/orthofinder/fasta/test/Results_Nov23/WorkingDirectory/SimpleTest.tre" - ok
    Test can run "dlcpar_search --version" - failed
    ERROR: Cannot run dlcpar_search
    Please check DLCpar is installed and that the executables are in the system path.
    
    Orthogroups have been inferred but the dependencies for inferring gene trees and
    orthologues have not been met. Please review previous messages for more information
    Any suggestion for me?

    Best Regards
    Zillur

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