tombo build_model estimate_reference global name 'motif' is not defined
DelphIONe opened this issue · comments
Hi!
I try to use the command tombo build_model estimate_reference but I obtain this error :
tombo build_model estimate_reference --fast5-basedirs fast5_gzip_single/ --tombo-model-filename noQ --processes 4 --corrected-group RawGenomeCorrected_001 --basecall-subgroups BaseCalled_custom
[15:36:46] Parsing Tombo index file(s).
[15:36:47] Calculating read coverage regions.
[15:36:47] Calculating read coverage.
[15:36:47] Extracting average k-mer levels.
100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 242/242 [00:28<00:00, 8.59it/s]
[15:37:16] Tabulating k-mer model statistics.
Traceback (most recent call last):
File "/usr/local/bin/tombo", line 11, in
load_entry_point('ont-tombo', 'console_scripts', 'tombo')()
File "/home/xxx/softs/tombo/tombo/main.py", line 250, in main
tombo_stats._est_ref_main(args)
File "/home/xxx/softs/tombo/tombo/tombo_stats.py", line 4799, in _est_ref_main
args.multiprocess_region_size, args.processes)
File "/home/xxx/softs/tombo/tombo/tombo_stats.py", line 1727, in estimate_kmer_model
all_kmer_mean_sds = tabulate_kmer_levels(all_reg_kmer_levels, min_kmer_obs)
File "/home/xxx/softs/tombo/tombo/tombo_stats.py", line 1479, in tabulate_kmer_levels
for kmer in product(DNA_BASES, repeat=kmer_width)
File "/home/xxx/softs/tombo/tombo/tombo_stats.py", line 1480, in
if motif is None or motif.matches_seq(''.join(kmer)))
NameError: global name 'motif' is not defined
Am I making a mistake somewhere ?
Thanks for your help,