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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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RuntimeError: maximum recursion depth exceeded in cmp #44

Closed opplatek closed 6 years ago

opplatek commented 6 years ago

During 2 out of 96 calculations I ran into an error RuntimeError: maximum recursion depth exceeded in cmp.

I am not a Python expert so I cannot suggest the best fix. Only what I found on Biostars (https://stackoverflow.com/questions/25105541/python-quicksort-runtime-error-maximum-recursion-depth-exceeded-in-cmp).

Adding lines import sys sys.setrecursionlimit(1500) (default value should be 1000) to shorah_mm.py fixed the issue but it is definitely not recommended nor optimal.

I am atttaching a shorah log from this failed calculation.

27_S27_bwamem.filtered.sorted.grp.indelRealigned.duplRem.recal.shorah.txt

Best, Jan

ozagordi commented 6 years ago

Hi Jan, thanks for your report. I don't want to seem harsh, but I must say that we plan to drop global reconstruction from shorah soon. Time has shown that, for this difficult problem, better alternatives exist. People tend to use shorah in unfavourable situations (low diversity spread over regions way longer than the reads), while its strength should be a sensitive detection of low frequency haplotypes in local mode. I will add wontfix label and close it, unless we find other reasons to reopen it.

But thanks again for your interest. Osvaldo