Unicycler works perfectly with test sequences but using hybrid assembly with Illumina short and MinION long reads get following Spades error:
SPAdes maximum k-mer: 127
Traceback (most recent call last):
File "/usr/local/bin/unicycler", line 33, in
sys.exit(load_entry_point('unicycler==0.5.0', 'console_scripts', 'unicycler')())
File "/Library/Python/3.9/site-packages/unicycler/unicycler.py", line 76, in main
graph = get_best_spades_graph(args.short1, args.short2, args.unpaired, args.out,
File "/Library/Python/3.9/site-packages/unicycler/spades_func.py", line 47, in get_best_spades_graph
kmer_range = get_kmer_range(kmers, short1, short2, short_unpaired, spades_dir, kmer_count,
File "/Library/Python/3.9/site-packages/unicycler/spades_func.py", line 363, in get_kmer_range
median_read_length = read_lengths[len(read_lengths) // 2 - 1]
IndexError: list index out of range
Using older version of Unicycler these sequences worked perfectly. ? not sure what the problem is. Grateful for any thoughts.
tomjevans
commented
11 months ago
Unicycler works perfectly with test sequences but using hybrid assembly with Illumina short and MinION long reads get following Spades error: SPAdes maximum k-mer: 127 Traceback (most recent call last): File "/usr/local/bin/unicycler", line 33, in
sys.exit(load_entry_point('unicycler==0.5.0', 'console_scripts', 'unicycler')())
File "/Library/Python/3.9/site-packages/unicycler/unicycler.py", line 76, in main
graph = get_best_spades_graph(args.short1, args.short2, args.unpaired, args.out,
File "/Library/Python/3.9/site-packages/unicycler/spades_func.py", line 47, in get_best_spades_graph
kmer_range = get_kmer_range(kmers, short1, short2, short_unpaired, spades_dir, kmer_count,
File "/Library/Python/3.9/site-packages/unicycler/spades_func.py", line 363, in get_kmer_range
median_read_length = read_lengths[len(read_lengths) // 2 - 1]
IndexError: list index out of range
Using older version of Unicycler these sequences worked perfectly. ? not sure what the problem is. Grateful for any thoughts.