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almiheenko / AGB

Interactive visualization of assembly graphs
https://almiheenko.github.io/AGB/
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ValueError: could not convert string to float: 'contig' #6

Open csuzhang opened 4 years ago

csuzhang commented 4 years ago

Hi: I ran the command : $ agb.py -i assembly/canu -a canu then got the following error: Traceback (most recent call last): File "/home/zhangjun/miniconda3/envs/AGB/bin/agb.py", line 154, in main() File "/home/zhangjun/miniconda3/envs/AGB/bin/agb.py", line 130, in main opts.output_dir, opts.input_fasta, opts.min_edge_len) File "/home/zhangjun/miniconda3/envs/AGB/bin/agb.py", line 67, in parse_assembler_output dict_edges, contig_edges, edges_fpath = parse_canu_output(input_dirpath, output_dirpath, min_edge_len) File "/home/zhangjun/miniconda3/envs/AGB/lib/python3.6/site-packages/agb_src/scripts/info_parser.py", line 22, in parse_canu_output dict_edges = parse_gfa(gfa_fpath, min_edge_len, input_dirpath, assembler="canu") File "/home/zhangjun/miniconda3/envs/AGB/lib/python3.6/site-packages/agb_src/scripts/graph_parser.py", line 289, in parse_gfa dict_edges = parse_canu_unitigs_info(input_dirpath, dict_edges) File "/home/zhangjun/miniconda3/envs/AGB/lib/python3.6/site-packages/agb_src/scripts/graph_parser.py", line 119, in parse_canu_unitigs_info coverage = int(float(fs[cov_col])) ValueError: could not convert string to float: 'contig'

Do you know what's wrong? Thank you

almiheenko commented 4 years ago

Hi,

Sorry for the delay! Probably there are some discrepancies in Canu output. Could you please send me the file "*.unitigs.layout.tigInfo" from assembly/canu folder (at least first 100 lines)? Thank you!