STRling
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quinlan-lab
L.start <= R.start
Hey, I get the following error for one of my samples in one of my projects
strling version: 0.5.1
using first reads in fragment_length_distribution calculation as there were not enough
Read 67332 bounds from results/strling/merge/tremor-ataxia-bounds.txt
fatal.nim(49) sysFatal
Error: unhandled exception: collect.nim(37, 12) `L.start <= R.start` [AssertionDefect]
I may help to fix this by providing any information you need!
This suggests that one of the rows in tremor-ataxia-bounds.txt is incorrect, with the left side of the locus being larger than the right. Happy to look through the file to find the offending locus if that would help. Or just do right column - left column and look for a negative to find the bad line. Was tremor-ataxia-bounds.txt generated with STRling?
yes tremor-ataxia-bounds.txt was generated by STRling merge as well as all predecessor .bin files by STRling extract.
I performed the column substraction and there are no negatives, but a lot of 0, which is also invalid?
I should have mentioned before: This is group calling and calling for the other files (except for my other issue) worked without any problems. Therefore I doubt that the reason behind this can be found in the bounds.txt. If you still want the file, I would be glad to share!
the error happens again, now with additional information
using first reads in fragment_length_distribution calculation as there were not enough
Read 15892 bounds from results/strling/merge/all-bounds.reduced.txt
fatal.nim(49) sysFatal
Error: unhandled exception: collect.nim(37, 12) `L.start <= R.start` (Record(6:94011350144480--1188996768):HWI-D00629:81:C7G26ANXX:3:2312:21292:22170, Record(6:94011349769008--1189373011):K00103:48:H3F5GBBXX:3:2128:28189:38381, (tid: 18, left: 1172137, left_most: 1171370, right: 1172151, right_most: 1172904, center_mass: 1172151, n_left: 0, n_right: 0, n_total: 0, repeat: "AT", name: "", force_report: true)) [AssertionDefect]