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ganlab / GALA

Long-reads Gap-free Chromosome-scale Assembler
MIT License
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newgenome throws ValueError: invalid literal for int() with base 10 #11

Closed fog-bank closed 3 years ago

fog-bank commented 3 years ago

Hello,

Thank you for developing GALA. I have a problem with newgenome as follows.

$ /media/Users/src/GALA/newgenome drafts.txt gathering
Traceback (most recent call last):
  File "/media/Users/src/GALA/newgenome", line 28, in <module>
    genomes(genomes=draft,gathering=gathering,gathering_name=name,outpath=output)
  File "/media/Users/src/GALA/src/new_genome.py", line 82, in genomes
    b=new_genome(cut_file=gathering+gathering_name+'_'+a+'_cuts.txt',old_genome=aa,out_path=outpath,name='new_'+a)
  File "/media/Users/src/GALA/src/new_genome.py", line 48, in new_genome
    i[base+'_'+str(h)+'_'+'awad']=e[base][int(g[j]):int(g[j+1])]
ValueError: invalid literal for int() with base 10: '6067162.0'

Single command mode throws a similar error. The content of gathering/gathering_draft_01_cuts.txt:

scaffold0003    6067162.0   4   3   0
...
scaffold0016    1397294.3333333333  3   2   0

I edited the *_cuts.txt files as all float values were trucated to integer values:

scaffold0003    6067162 4   3   0
...
scaffold0016    1397294 3   2   0

Then newgenome exited successfully. However, will the final result be expected?

Best

fog-bank commented 3 years ago

Sorry, I should use python2. python2 newgenome Thanks.