How to solve logic inconsistency?

[Keltonc]

Hi,

I have received the following error message when running minimap2 step in purge_haplotigs.

[M::main::12.417*0.75] loaded/built the index for 7855 target sequence(s)
[M::mm_mapopt_update::14.333*0.78] mid_occ = 412
[M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 7855
[M::mm_idx_stat::15.312*0.79] distinct minimizers: 96558399 (43.15% are singletons); average occurrences: 6.700; average spacing: 5.347; total length: 3458789385
[WARNING] logic inconsistency in mm_est_err(). Please contact the developer.
[WARNING] logic inconsistency in mm_est_err(). Please contact the developer.
[WARNING] logic inconsistency in mm_est_err(). Please contact the developer.
[WARNING] logic inconsistency in mm_est_err(). Please contact the developer.
[WARNING] logic inconsistency in mm_est_err(). Please contact the developer.
[WARNING] logic inconsistency in mm_est_err(). Please contact the developer.
[WARNING] logic inconsistency in mm_est_err(). Please contact the developer.
[WARNING] logic inconsistency in mm_est_err(). Please contact the developer.
[WARNING] logic inconsistency in mm_est_err(). Please contact the developer.
[WARNING] logic inconsistency in mm_est_err(). Please contact the developer.
.....

I'm now using minimap2/2.26 and cannot find any solution in both purge_haplotigs and minimap2 github. Can anyone help me with this issue? Thank you so much.

[xiekunwhy]

Hi,

Have you solved this problem?

I got these errors when using greenhill (https://github.com/ShunOuchi/GreenHill/issues/19), after consuming a lot of memory, minimap2 (2.26-r1175) stop with these error warnings

[M::mm_idx_gen::48.4871.61] collected minimizers [M::mm_idx_gen::51.1522.66] sorted minimizers [M::main::51.1522.66] loaded/built the index for 723 target sequence(s) [M::mm_mapopt_update::52.1712.63] mid_occ = 2081 [M::mm_idx_stat] kmer size: 15; skip: 10; is_hpc: 0; #seq: 723 [M::mm_idx_stat::52.697*2.61] distinct minimizers: 40707316 (0.11% are singletons); average occurrences: 6.839; average spacing: 5.324; total length: 1482199409 [WARNING] logic inconsistency in mm_est_err(). Please contact the developer. [WARNING] logic inconsistency in mm_est_err(). Please contact the developer. [WARNING] logic inconsistency in mm_est_err(). Please contact the developer. [WARNING] logic inconsistency in mm_est_err(). Please contact the developer. [WARNING] logic inconsistency in mm_est_err(). Please contact the developer. [WARNING] logic inconsistency in mm_est_err(). Please contact the developer. [WARNING] logic inconsistency in mm_est_err(). Please contact the developer. [WARNING] logic inconsistency in mm_est_err(). Please contact the developer. [WARNING] logic inconsistency in mm_est_err(). Please contact the developer. ........ [WARNING] logic inconsistency in mm_est_err(). Please contact the developer. [WARNING] logic inconsistency in mm_est_err(). Please contact the developer. [WARNING] logic inconsistency in mm_est_err(). Please contact the developer. [WARNING] logic inconsistency in mm_est_err(). Please contact the developer. minimap2: align.c:806: mm_align1: Assertion `qe1 <= qlen' failed. Aborted (core dumped) minimap2 finished.

Best, Kun