wutron / dlcpar Goto Github PK

Hi!

I am trying to install-do a test run on one of my gene trees but I did not manage to succeed so far and I am getting the following error.

This is the command I am using:

dlcpar landscape -s ../../FullPhylogeny/concatenated.nex.treefile.rooted -S species_map.tab ../unrooted/aligned_4148.fasta.treefile

And the error is the following:

IOError: [Errno 2] No such file or directory: '../unrooted/aligned_4148.fasta.treefile.dlcscape.info'

Should this not be actually the output file? I have no idea what is going on, any help would be very welcome.

Thanks in advance!

Hi,

I met an error when executing dlcpar dp on a rooted RAxML tree. It would be grateful if you can provide me any hints to this problem. Thanks!

Hui

Command I use:

timeout 300 dlcpar dp -s dlcpar.sptree -S dlcpar.txt.smap combine.clean.tre.root --output_format 3t  -D 2 -L 1 -C 0.5  2>stderr.txt > stdout.txt

$more stdout.txt

Found
Found
...

$more stderr.txt

Traceback (most recent call last):
  File "/nfs/liuhui/.conda/envs/dlcpar/bin/dlcpar", line 94, in <module>
    sys.exit(main())
  File "/nfs/liuhui/.conda/envs/dlcpar/bin/dlcpar", line 91, in main
    mod.run()
  File "/nfs/liuhui/.conda/envs/dlcpar/lib/python2.7/site-packages/dlcpar/commands/dp.py", line 280, in run
    log=out_log)
  File "/nfs/liuhui/.conda/envs/dlcpar/lib/python2.7/site-packages/dlcpar/recondp.py", line 61, in dlc_recon
    return reconer.recon()
  File "/nfs/liuhui/.conda/envs/dlcpar/lib/python2.7/site-packages/dlcpar/recondp.py", line 163, in recon
    self._infer_locus_map()
  File "/nfs/liuhui/.conda/envs/dlcpar/lib/python2.7/site-packages/dlcpar/recondp.py", line 225, in _infer_locus_map
    self._infer_opt_locus_map(locus_maps, subtrees)
  File "/nfs/liuhui/.conda/envs/dlcpar/lib/python2.7/site-packages/dlcpar/recondp.py", line 1177, in _infer_opt_locus_map
    dp_table = self._dp_compute(locus_maps)
  File "/nfs/liuhui/.conda/envs/dlcpar/lib/python2.7/site-packages/dlcpar/recondp.py", line 1414, in _dp_compute
    assert mincost != INF, (top_loci, lst)
AssertionError: ((1, 2, 3, 4, 5, 6), [((1, 2, 3, 4, 5, 6), inf, 0)])

Would it be possible to make your code Python3-compatible? Currently there are several print statements scattered throughout the code that are not compatible unless they are changed to print functions. So I get errors like this:

dlcpar
Traceback (most recent call last):
  File "./bin/dlcpar", line 11, in <module>
    from dlcpar import common
  File "/home/cooketho/lib/python2.7/site-packages/dlcpar/common.py", line 5, in <module>
    from rasmus import treelib, util
  File "/home/cooketho/lib/python2.7/site-packages/dlcpar/deps/rasmus/treelib.py", line 1089
    print i, parentid
          ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(i, parentid)?

I can fix it by changing the following line in bin/dlcpar, but why not just make whole code compatible?

#!/usr/bin/env python

#!/usr/bin/env python2.7

Hi

When I try to run the setup script to install dlcpar then I get an error:

error: package directory 'python/dlcpar/deps/rasmus/ply' does not exist

and so am unable to install this version and when I check in the repository this directory is indeed missing.

All the best
David

Hi

I intend to use the release version on your website (https://www.cs.hmc.edu/~yjw/software/dlcpar/) as you suggested. However, I was just trying the github version and I encountered a problem where dlcpar seems to be trying to write to a file path that doesn't exist.

I've attached a test case, if I run the following command inside the attached directory using the command:

dlcpar_search -s Trees_ids/SpeciesTree_ids_0_rooted.txt -S Trees_ids/GeneMap.smap -D 1 -C 0.125 Trees_ids/OG0000000_tree_id.txt -O dlcpar/OG0000000_tree_id

Then I get the following error:

Traceback (most recent call last):
File "/usr/local/bin/dlcpar_search", line 209, in
sys.exit(main())
File "/usr/local/bin/dlcpar_search", line 201, in main
phyloDLC.write_dlcoal_recon(out, coal_tree, maxrecon)
File "/usr/local/lib/python2.7/dist-packages/dlcpar/deps/compbio/phyloDLC.py", line 350, in write_dlcoal_recon
recon.write(filename, coal_tree, exts, filenames, filestreams)
File "/usr/local/lib/python2.7/dist-packages/dlcpar/deps/compbio/phyloDLC.py", line 178, in write
rootData=True)
File "/usr/local/lib/python2.7/dist-packages/dlcpar/deps/rasmus/treelib.py", line 602, in write_newick
write_newick(self, util.open_stream(out, "w"),
File "/usr/local/lib/python2.7/dist-packages/dlcpar/deps/rasmus/util.py", line 1171, in open_stream
stream = open(filename, mode)
IOError: [Errno 2] No such file or directory: 'Trees_ids/OG0000000_tree_id.txtdlcpar/OG0000000_tree_id.coal.tree'

I.e. it seems to be concatenating the paths incorrectly. This ran fine for me with version 0.9.1.

Thanks for your help
David
dlcpar_output_error.tar.gz

Hello,

After cloning the git repository and running 'python setup.py install --prefix home/username/, I get the syntax errors described in the attached picture.

Can you help me understand these errors?

Thank you for your time.

Hi

With some (large) trees I get an error "maximum recursion depth exceeded". The command I used was:
"dlcpar_search -s SpeciesTree_ids_0_rooted.txt -S GeneMap.smap OG0000007_tree_id.txt" with the attached files. The output was:

Traceback (most recent call last):
File "/usr/local/bin/dlcpar_search", line 236, in
sys.exit(main())
File "/usr/local/bin/dlcpar_search", line 206, in main
log=log_out)
File "/usr/local/lib/python2.7/dist-packages/dlcpar/simplerecon.py", line 39, in dlc_recon
return reconer.recon(nsearch, nconverge).get_dict()
File "/usr/local/lib/python2.7/dist-packages/dlcpar/simplerecon.py", line 83, in recon
proposal = self.proposer.init_proposal()
File "/usr/local/lib/python2.7/dist-packages/dlcpar/simplerecon.py", line 249, in init_proposal
self._recon = self._recon_lca(self._locus_search.get_tree().copy())
File "/usr/local/lib/python2.7/dist-packages/dlcpar/simplerecon.py", line 283, in _recon_lca
self._gene2species)
File "/usr/local/lib/python2.7/dist-packages/dlcpar/deps/compbio/phylo.py", line 130, in reconcile
walk(gtree.root)
File "/usr/local/lib/python2.7/dist-packages/dlcpar/deps/compbio/phylo.py", line 124, in walk

......
......
etc
.....
File "/usr/local/lib/python2.7/dist-packages/dlcpar/deps/rasmus/treelib.py", line 83, in recurse
func(child, *args)
File "/usr/local/lib/python2.7/dist-packages/dlcpar/deps/compbio/phylo.py", line 124, in walk
node.recurse(walk)
File "/usr/local/lib/python2.7/dist-packages/dlcpar/deps/rasmus/treelib.py", line 83, in recurse
func(child, *args)
RuntimeError: maximum recursion depth exceeded

Thanks
David
error_files.zip