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rrwick / Unicycler

hybrid assembly pipeline for bacterial genomes
GNU General Public License v3.0
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Graph file from the Flye assembler seems to cause error when used for "pilon_polish.py" #165

Open ilnamkang opened 5 years ago

ilnamkang commented 5 years ago

Hi,

I'm trying to improve assembly quality of my genomes by applying Unicycler to the output of the Flye assembler (https://github.com/fenderglass/Flye).

I've tried two different ways, using the graph file from the Flye assembler (assembly_graph.gfa). (1) Using the "--existing_long_read_assembly" option when running unicycler (2) Using the graph file as an input for the "pilon_polish.py" script

The first approach (using "--existing_long_read_assembly" option) was successful and produced a little bit improved assembly without any errors.

But, the second approach (using "pilon_polish.py" script) caused an error just after dependency check. The error message is attached below.

Traceback (most recent call last): File "/home/memb-main/Unicycler/scripts/pilon_polish.py", line 224, in main() File "/home/memb-main/Unicycler/scripts/pilon_polish.py", line 41, in main graph = unicycler.assembly_graph.AssemblyGraph(args.input, None) File "/usr/local/lib/python3.4/dist-packages/unicycler/assembly_graph.py", line 63, in init self.load_from_gfa(filename) File "/usr/local/lib/python3.4/dist-packages/unicycler/assembly_graph.py", line 116, in load_from_gfa num = int(line_parts[1]) ValueError: invalid literal for int() with base 10: 'contig_1'

How can I avoid this error?

Thanks.

ehelegam commented 5 years ago

The Python code to load GFA files (see below) requires that the segment names are integers. I solved this issue by replacing original GFA's segment names (i.e. 'edge_1' --> '1'). Good luck.

def load_from_gfa(self, filename): """ Loads a Graph from a GFA file. It does not load any GFA file, but makes some restrictions: 1) The segment names must be integers. 2) The depths should be stored in a dp tag. 3) All link overlaps are the same (equal to the graph overlap value). """