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cbg-ethz / shorah

Repo for the software suite ShoRAH (Short Reads Assembly into Haplotypes)
GNU General Public License v3.0
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ShoRAH.py error #43

Closed woodford87 closed 6 years ago

woodford87 commented 6 years ago

Hi, I've got the following error when running shorah.py against a 10KB genome with an illumina data set.

Traceback (most recent call last): File "./shorah.py", line 139, in <module> alpha=args.a, keep_files=args.k, seed=args.S) File "/Users/lukewoodford/shorah/lib/python3.6/site-packages/shorah_dec.py", line 438, in main beg = int(parts[-2]) ValueError: invalid literal for int() with base 10: 'gb'

The command line used to run this was:

./shorah.py -b sorted.bam -f ref.fa

Can anyone help with this error?

woodford87 commented 6 years ago

I've managed to progress beyond this point by removing any '.' in my ref however, I am not getting the following error

Traceback (most recent call last): File "./shorah.py", line 172, in <module> shorah_mm.main('%s_cor.rest' % in_stem, maxhaplo=2000) File "/Users/lukewoodford/shorah/lib/python3.6/site-packages/shorah_mm.py", line 703, in main descList = findDescendants(graph) File "/Users/lukewoodford/shorah/lib/python3.6/site-packages/shorah_mm.py", line 317, in findDescendants getDesc(i) File "/Users/lukewoodford/shorah/lib/python3.6/site-packages/shorah_mm.py", line 311, in getDesc descList[node].update(getDesc(x)) File "/Users/lukewoodford/shorah/lib/python3.6/site-packages/shorah_mm.py", line 311, in getDesc descList[node].update(getDesc(x)) File "/Users/lukewoodford/shorah/lib/python3.6/site-packages/shorah_mm.py", line 311, in getDesc descList[node].update(getDesc(x)) [Previous line repeated 992 more times] File "/Users/lukewoodford/shorah/lib/python3.6/site-packages/shorah_mm.py", line 299, in getDesc if len(descList[node]) > 0: RecursionError: maximum recursion depth exceeded in comparison

Is anyone able to shed any light on this? I tried changing the max haplotypes in the shorah.py script (line 172) to 2000, instead of the default 200, but this hasn't helped.

ozagordi commented 6 years ago

Hi. Not sure how to help here. I must say that we don't really support/promote global reconstruction with shorah anymore, see also A word of caution here. You might be luckier with other tools, but always keeping in mind the intrinsic limitations of the approach. I'm closing this now because we plan to remove global reconstruction from shorah anyway.

Thanks for understanding.