Hi there,
I am using Rebaler for the first time, trying it on a Google Colab script. the script installs minimap2, racon, biopython and Rebaler. The installation fails but I could patch it with this https://github.com/rrwick/Rebaler/issues/12#issuecomment-884261417
I tried to run it both by using the installed program
rebaler <a.reference.fasta> <a.big.fastq.with.all.reads>
And the python script directly
<path/to/rebaler-runner.py> <a.reference.fasta> <a.big.fastq.with.all.reads>
In both cases I got the error message
File "/content/Rebaler/rebaler-runner.py", line 9, in
main()
File "/content/Rebaler/rebaler/main.py", line 89, in main
reference, ref_names, circularity, ref_seqs = load_reference(args.reference)
File "/content/Rebaler/rebaler/main.py", line 105, in load_reference
log.log_explanation('This reference sequence will be used as a template for the Rebaler '
File "/content/Rebaler/rebaler/log.py", line 65, in log_explanation
for line in textwrap.wrap(text, width=terminal_width - 1):
File "/usr/lib/python3.7/textwrap.py", line 379, in wrap
return w.wrap(text)
File "/usr/lib/python3.7/textwrap.py", line 354, in wrap
return self._wrap_chunks(chunks)
File "/usr/lib/python3.7/textwrap.py", line 248, in _wrap_chunks
raise ValueError("invalid width %r (must be > 0)" % self.width)
ValueError: invalid width -1 (must be > 0)
Any pointers?
rrwick
