Issue with gapless.py extend

[pclee2007]

Hi, I got an error in running gapless.sh (in the step of gapless.py extend);

logs/gapless_extend.log describes the following error, "Traceback (most recent call last): File "/analysis/program/gapless.py", line 13362, in main(sys.argv[1:]) File "/analysis/program/gapless.py", line 13228, in main GaplessExtend(args[0], prefix, min_length_contig_break, large_reads) UnboundLocalError: local variable 'large_reads' referenced before assignment"

Thanks, Pyung Cheon

[SaelinB]

I had the same issue and solved it by using the conda installation with python 3.9.6 and pandas 1.5.3

[Dogrinev]

Posted an alternative solution to this in https://github.com/schmeing/gapless/issues/18#issuecomment-1910497051