Unknown error in resquiggle command

[CarolinaA09]

Hi, I am using this command to resquiggle my RNA data:

remora dataset prepare pod5_dir file.bam --output-path mod_chunks --refine-kmer-level-table 5mer_levels_v1.txt --refine-rough-rescale --motif CG 0 --mod-base m 5mC --reverse-signal --overwrite

But, I am getting an error. I am not sure what it is about:

Traceback (most recent call last):
File "/nas/longleaf/home/caroe/.local/bin/remora", line 8, in
sys.exit(run())
File "/nas/longleaf/home/caroe/.local/lib/python3.10/site-packages/remora/main.py", line 71, in run
cmd_func(args)
File "/nas/longleaf/home/caroe/.local/lib/python3.10/site-packages/remora/parsers.py", line 290, in run_dataset_prepare
sig_map_refiner = SigMapRefiner(
File "", line 17, in init
File "/nas/longleaf/home/caroe/.local/lib/python3.10/site-packages/remora/refine_signal_map.py", line 294, in post_init
self.load_kmer_table()
File "/nas/longleaf/home/caroe/.local/lib/python3.10/site-packages/remora/refine_signal_map.py", line 230, in load_kmer_table
self.kmer_len = len(kmer_fp.readline().split()[0])
IndexError: list index out of range

I would greatly appreciate your input.

Kind regards,

CA

[marcus1487]

It looks like the first line of your file 5mer_levels_v1.txt is empty. Could you check that this file is not empty?

[CarolinaA09]

Indeed thanks! It was improperly retrieved! Thank you.