direct-RNA resquiggle error and there are 99.9% reads unsuccessfully processed

[RainaYin-sys]

Hi: I got an error in a file named unexpected_tombo_errors.1252.err when I run the direct-RNA resquiggle. The command and error are as follows:

tombo resquiggle ${sigle_fast5_dir} ${transcriptome} --processes 10 --num-most-common-errors 5 --rna

BaseCalled_template:::/data1/research/methylation_rna/tombo/test/citrus.sigle_fast5_ln/811e2377-94c8-4206-9efc-c65692fc4194.fast5 ::: Traceback (most recent call last): File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/tombo_helper.py", line 94, in banded_traceback return c_banded_traceback(*args, **kwargs) File "tombo/_c_dynamic_programming.pyx", line 305, in tombo._c_dynamic_programming.c_banded_traceback NotImplementedError: Read event to sequence alignment extends beyond bandwidth

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 1575, in _resquiggle_worker map_res, rsqgl_params, fast5_fn, all_raw_signal) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 1491, in run_rsqgl_iters seq_samp_type=seq_samp_type) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 1168, in resquiggle_read seq_samp_type=seq_samp_type, reg_id=map_res.align_info.ID) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 1038, in find_adaptive_base_assignment rsqgl_params.band_bound_thresh) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/tombo_helper.py", line 96, in banded_traceback raise TomboError(unicode(e)) tombo.tombo_helper.TomboError: Read event to sequence alignment extends beyond bandwidth

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 1583, in _resquiggle_worker map_res, save_params, fast5_fn, all_raw_signal) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 1491, in run_rsqgl_iters seq_samp_type=seq_samp_type) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 1168, in resquiggle_read seq_samp_type=seq_samp_type, reg_id=map_res.align_info.ID) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 1028, in find_adaptive_base_assignment fwd_pass, fwd_pass_move, band_event_starts, shifted_z_scores = run_fwd_pass() File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 899, in run_fwd_pass mapped_start_offset, rsqgl_params, events_per_base) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 676, in _get_masked_start_fwd_pass shifted_z_scores[seq_pos,:] = get_start_mask_z_score(seq_pos, event_pos) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 661, in get_start_mask_z_score event_vals, r_ref_means[seq_pos], r_ref_sds[seq_pos], IndexError: index 409 is out of bounds for axis 0 with size 409

BaseCalled_template:::/ifs/TJPROJ3/PB/personal_dir/yinxiaoru/research/methylation_rna/tombo/all_reads_test/citrus.sigle_fast5_ln/d56e39ac-672d-4968-830e-e65c27173fa0.fast5 ::: Traceback (most recent call last): File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/tombo_helper.py", line 94, in banded_traceback return c_banded_traceback(*args, **kwargs) File "tombo/_c_dynamic_programming.pyx", line 305, in tombo._c_dynamic_programming.c_banded_traceback NotImplementedError: Read event to sequence alignment extends beyond bandwidth

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 1575, in _resquiggle_worker map_res, rsqgl_params, fast5_fn, all_raw_signal) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 1491, in run_rsqgl_iters seq_samp_type=seq_samp_type) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 1168, in resquiggle_read seq_samp_type=seq_samp_type, reg_id=map_res.align_info.ID) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 1038, in find_adaptive_base_assignment rsqgl_params.band_bound_thresh) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/tombo_helper.py", line 96, in banded_traceback raise TomboError(unicode(e)) tombo.tombo_helper.TomboError: Read event to sequence alignment extends beyond bandwidth

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 1583, in _resquiggle_worker map_res, save_params, fast5_fn, all_raw_signal) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 1491, in run_rsqgl_iters seq_samp_type=seq_samp_type) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 1168, in resquiggle_read seq_samp_type=seq_samp_type, reg_id=map_res.align_info.ID) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 1028, in find_adaptive_base_assignment fwd_pass, fwd_pass_move, band_event_starts, shifted_z_scores = run_fwd_pass() File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 899, in run_fwd_pass mapped_start_offset, rsqgl_params, events_per_base) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 676, in _get_masked_start_fwd_pass shifted_z_scores[seq_pos,:] = get_start_mask_z_score(seq_pos, event_pos) File "/ifs/TJPROJ3/PB/softwares/Anacondas/miniconda3/envs/tombo/lib/python3.6/site-packages/tombo/resquiggle.py", line 661, in get_start_mask_z_score event_vals, r_ref_means[seq_pos], r_ref_sds[seq_pos], IndexError: index 442 is out of bounds for axis 0 with size 442

Thanks.