Bioconda version crashing

[apredeus]

Hello Ryan,

I'm getting the same error with both the latest Bioconda version of Rebaler and the cloned latest version from repository. This is the part of the log where it crashes. Any suggestions? Thank you in advance!

Loading reads... 119,222 reads
Aligning reads to reference with minimap2... 112,226 initial alignments
105.46x depth
Culling alignments to a non-redundant set... 710 alignments remain

Constructing unpolished assembly:

contig_1:
Traceback (most recent call last):
File "/pub37/alexp/Rebaler/rebaler-runner.py", line 9, in
main()
File "/pub37/alexp/Rebaler/rebaler/rebaler.py", line 74, in main
print_partitions(ref_names, partitions, nicknames, ref_seqs)
File "/pub37/alexp/Rebaler/rebaler/rebaler.py", line 261, in print_partitions
ref_seqs[name])
File "/pub37/alexp/Rebaler/rebaler/alignment.py", line 108, in get_read_seq_by_ref_coords
if ref_seq[ref_pos] == self.read_seq[read_pos]:
IndexError: string index out of range

[rrwick]

Hi Alex,

I'm not certain, but this may be due to a mismatch with Racon versions. The current version of Rebaler requires a current version of Racon (1.0+, I think) because the usage is different from older versions.

If you have a current version of both Rebaler and Racon and still see the error, let me know!

Ryan