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schmeing / gapless

Gapless provides combined scaffolding, gap-closing and assembly correction with long reads
MIT License
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Gapless extend local variable error #18

Open SaelinB opened 8 months ago

SaelinB commented 8 months ago

Hello, I am using gapless with python version 3.9.6, and I get this error on the extend step:

Traceback (most recent call last):
File "/home/student.unimelb.edu.au/sbjornson/opt/gapless/gapless.py", line 13362, in
main(sys.argv[1:])
File "/home/student.unimelb.edu.au/sbjornson/opt/gapless/gapless.py", line 13228, in main
GaplessExtend(args[0], prefix, min_length_contig_break, large_reads)
UnboundLocalError: local variable 'large_reads' referenced before assignment

Any ideas on how to fix?

SaelinB commented 8 months ago

I actually figured it out, I needed to switch to the conda version, and then install python 3.9.6 and pandas version 1.5.3.

Dogrinev commented 8 months ago

Tried the solution posted by SaelinB but did not work for me - I have all python packages set to the tested versions listed on the main page, tried pandas as 1.3.1 and 1.5.3 and get the error:

"UnboundLocalError: local variable 'large_reads' referenced before assignment"

Dogrinev commented 8 months ago

I found a solution for anyone that runs into this issue - the bug seems to be caused by a missing baseline definition of the 'large_reads' variable in the GaplessExtend function. I borrowed a line of code from GaplessScaffold which seemed to be missing in the extend function.

Manually insert a new line after line 13199 (min_length_contig_break = 1200) which should read 'large_reads = False'. This gives the large_reads variable a baseline definition and will be flipped to true if the large reads flag is set in the function initially. Pipeline worked for me after making this adjustment.