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mikolmogorov / Ragout

Chromosome-level scaffolding using multiple references
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work flow stuck #53

Closed mostafaabuzaid25 closed 4 years ago

mostafaabuzaid25 commented 4 years ago

I dont know what happen always stuck here.

[20:33:39] INFO: Reading contigs file [20:33:52] INFO: Detecting chimeric adjacencies [20:35:05] INFO: Stage "10000" [20:35:05] INFO: Removing chimeric adjacencies [20:35:05] INFO: Inferring missing adjacencies Traceback (most recent call last): File "/public/home/jmwu/soft/Ragout/bin/ragout", line 32, in sys.exit(main()) File "/public/home/jmwu/soft/Ragout/ragout/main.py", line 290, in main _run_ragout(args) File "/public/home/jmwu/soft/Ragout/ragout/main.py", line 214, in _run_ragout adjacencies = adj_inferer.infer_adjacencies() File "/public/home/jmwu/soft/Ragout/ragout/breakpoint_graph/inferer.py", line 44, in infer_adjacencies chosen_edges.extend(self._process_component(subgraph)) File "/public/home/jmwu/soft/Ragout/ragout/breakpoint_graph/inferer.py", line 77, in _process_component adjacency = subgraph.to_weighted_graph(self.phylogeny) File "/public/home/jmwu/soft/Ragout/ragout/breakpoint_graph/breakpoint_graph.py", line 104, in to_weighted_graph g.add_nodes_from(self.bp_graph.nodes) File "/public/home/jmwu/miniconda2/lib/python2.7/site-packages/networkx/classes/graph.py", line 511, in add_nodes_from for n in nodes: TypeError: 'instancemethod' object is not iterable

also with repeat algorithm

[02:20:43] INFO: Starting Ragout v2.2

[02:20:44] INFO: Running withs synteny block sizes '[10000, 500, 100]' [02:20:44] INFO: Extracting FASTA from HAL [02:21:26] INFO: Converting HAL to MAF [03:57:07] INFO: Extracting synteny blocks from MAF [03:57:12] INFO: Running maf2synteny module [04:00:28] INFO: Inferring phylogeny from synteny blocks data [04:00:28] INFO: Reading /public/home/jmwu/ref2/Chilo_chr/hal-workdir/100/blocks_coords.txt [04:00:32] INFO: "Trichoplusia" synteny blocks coverage: 13.71% [04:00:33] INFO: "Chilo" synteny blocks coverage: 25.03% [04:00:33] INFO: "Bomobyx" synteny blocks coverage: 12.87% [04:00:33] WARNING: Some genomes have low synteny block coverage - results can be inaccurate. Possible reasons:

  1. Genome is too distant from others
  2. Synteny block parameters are chosen incorrectly Try to change synteny blocks paramsters or remove this genome from the comparison [04:00:44] INFO: Inferred tree: ('Bomobyx' : 2401.0, ('Chilo' : 1830.0, 'Trichoplusia' : 3906.0) : 2401.0) [04:00:44] INFO: 'Trichoplusia' is chosen as a naming reference [04:00:44] INFO: Processing permutation files [04:00:44] INFO: Reading /public/home/jmwu/ref2/Chilo_chr/hal-workdir/10000/blocks_coords.txt [04:00:44] INFO: "Trichoplusia" synteny blocks coverage: 29.8% [04:00:44] INFO: "Chilo" synteny blocks coverage: 28.3% [04:00:44] INFO: "Bomobyx" synteny blocks coverage: 31.03% [04:00:44] WARNING: Some genomes have low synteny block coverage - results can be inaccurate. Possible reasons:
  3. Genome is too distant from others
  4. Synteny block parameters are chosen incorrectly Try to change synteny blocks paramsters or remove this genome from the comparison [04:00:44] INFO: Reading /public/home/jmwu/ref2/Chilo_chr/hal-workdir/500/blocks_coords.txt [04:00:45] INFO: "Trichoplusia" synteny blocks coverage: 18.79% [04:00:46] INFO: "Chilo" synteny blocks coverage: 27.37% [04:00:46] INFO: "Bomobyx" synteny blocks coverage: 19.35% [04:00:46] WARNING: Some genomes have low synteny block coverage - results can be inaccurate. Possible reasons:
  5. Genome is too distant from others
  6. Synteny block parameters are chosen incorrectly Try to change synteny blocks paramsters or remove this genome from the comparison [04:00:50] INFO: Reading /public/home/jmwu/ref2/Chilo_chr/hal-workdir/100/blocks_coords.txt [04:00:54] INFO: "Trichoplusia" synteny blocks coverage: 13.71% [04:00:54] INFO: "Chilo" synteny blocks coverage: 25.03% [04:00:54] INFO: "Bomobyx" synteny blocks coverage: 12.87% [04:00:54] WARNING: Some genomes have low synteny block coverage - results can be inaccurate. Possible reasons:
  7. Genome is too distant from others
  8. Synteny block parameters are chosen incorrectly Try to change synteny blocks paramsters or remove this genome from the comparison [04:01:07] INFO: Reading /public/home/jmwu/ref2/Chilo_chr/hal-workdir/100/blocks_coords.txt [04:01:11] INFO: "Trichoplusia" synteny blocks coverage: 13.71% [04:01:12] INFO: "Chilo" synteny blocks coverage: 25.03% [04:01:12] INFO: "Bomobyx" synteny blocks coverage: 12.87% [04:01:12] WARNING: Some genomes have low synteny block coverage - results can be inaccurate. Possible reasons:
  9. Genome is too distant from others
  10. Synteny block parameters are chosen incorrectly Try to change synteny blocks paramsters or remove this genome from the comparison [04:01:18] INFO: Resolving repeats Traceback (most recent call last): File "/public/home/jmwu/soft/Ragout/bin/ragout", line 32, in sys.exit(main()) File "/public/home/jmwu/soft/Ragout/ragout/main.py", line 290, in main _run_ragout(args) File "/public/home/jmwu/soft/Ragout/ragout/main.py", line 191, in _run_ragout stage.ref_indels, phylogeny) File "/public/home/jmwu/soft/Ragout/ragout/breakpoint_graph/permutation.py", line 87, in init repeats, phylogeny, draft_names) File "/public/home/jmwu/soft/Ragout/ragout/breakpoint_graph/repeat_resolver.py", line 75, in resolve_repeats profiles = _split_into_profiles(by_genome, repeats, phylogeny) File "/public/home/jmwu/soft/Ragout/ragout/breakpoint_graph/repeat_resolver.py", line 180, in _split_into_profiles edges = _max_weight_matching(graph) File "/public/home/jmwu/soft/Ragout/ragout/breakpoint_graph/repeat_resolver.py", line 365, in _max_weight_matching for v1, v2 in edges: ValueError: too many values to unpack
mikolmogorov commented 4 years ago

Hi,

It might be inconsistency between networkx package versions. I recommend to try the bioconda package.

Best, Mikhail