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Kinggerm / GetOrganelle

Organelle Genome Assembly Toolkit (Chloroplast/Mitocondrial/ITS)
GNU General Public License v3.0
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Problems with canu-produced gfa processing #265

Open Hoberti opened 1 year ago

Hoberti commented 1 year ago

Describe the bug I am using getorganelle for obtaining a circular mitochondria and I am getting this message. The gfa is from a canu assembly. Could you help me please? What could be wrong in the gfa?

2023-05-10 17:12:23,670 - ERROR: Traceback (most recent call last): File "getorganelle/bin/slim_graph.py", line 976, in main this_assembly = Assembly(graph_file=fas_file, min_cov=options.min_depth, max_cov=options.max_depth) File "getorganelle/lib/python3.8/site-packages/GetOrganelleLib/assembly_parser.py", line 619, in init super(Assembly, self).init(graph_file=graph_file, min_cov=min_cov, max_cov=max_cov) File "getorganelle/lib/python3.8/site-packages/GetOrganelleLib/assembly_parser.py", line 258, in init self.parse_gfa(graph_file, min_cov=min_cov, max_cov=max_cov) File "/getorganelle/lib/python3.8/site-packages/GetOrganelleLib/assembly_parser.py", line 338, in parse_gfa raise ProcessingGraphFailed(vertex_name + " has unmatched sequence length as noted!") GetOrganelleLib.assembly_parser.ProcessingGraphFailed: 'tig00000001 has unmatched sequence length as noted!'

2023-05-10 17:12:23,810 - ERROR: Traceback (most recent call last): File "getorganelle/bin/get_organelle_from_assembly.py", line 1019, in main exit() File "getorganelle/lib/python3.8/_sitebuiltins.py", line 26, in call raise SystemExit(code) SystemExit: None

Total cost 2.66 s

The following command was executed: get_organelle_from_assembly.py -o getorgan -F embplant_mt -g Mito.unitigs.gfa

JianjunJin commented 1 year ago

Hi @Hoberti , Sorry for the long delay. The support for .gfa files has been tested for SPAdes, flye, and hifiasm, as well as tools that produce a similar style of gfa. I just checked a `.unitigs.gfafile produced bycanuon my hand and found it contains no sequence, while the sequences were stored in a concomitant*.unitigs.fastafile. Something must be done to accommodate this style ofgfa+fasta. I will leave it open until I add the feature. But it won't be very fast bc I'm swamped by other projects recently. For now, you may tryflye` instead. Thank you for posting this issue!