Batch 1 populations: src/utils.h:121: double GtLiks::at(std::size_t) const: Assertion `has_lik(gt)' failed.

[Mattia De Vivo]

Hello there,

I was using the denovo_map.pl and everything went smooth until the populations step (with the error written as the name of this topic).

I leave the log and the pop map used here, I honestly have no idea what I did wrong, although it seems to me that the "r" parameter in population caused it (the command works smooth if I remove it, and it doesn't matter if I set it at "80", "0.8" or "0.80" given the fact it stops the execution anyway).

Thanks in advance for the answer and sorry for the bother.

Best wishes,

Mattia

[Catchen, Julian]

Hi Mattia,

 

I would guess that the ‘--vcf-all’ flag to populations is causing the problem, as it is new to release 2.62 and hasn’t seen a lot of use yet.

 

Best,

 

julian

[Mattia De Vivo]

Hi Julian,

I guess the same. I removed entirely the --vcf command and it works, while it bugs even if I put just --vcf together with the r80 (it doesn't if I remove the latter).

I want also to say I got this error in Fedora; I did the the same with a Mac and I got no issue (although with a different dataset).

I'll try to do the same procedure with the same dataset on the mac and I'll check what happens.

Best wishes,

Mattia

[Mattia De Vivo]

Hi,

I did it on the mac and it gave me no issue, even by putting other flags (i.e., --radpainter).

I'm not sure why it bugs on Fedora.

I also leave the mac log here.

Best wishes,

Mattia

[Mattia De Vivo]

Hi,

I understood the issue (quite a simple one): my Fedora computer doesn't have enough RAM to output the VCF for my dataset.

Best wishes,

Mattia

[Pavel Škaloud]

Hi all,
I confirm this is a memory problem if many options are used in the population. Either increasing memory or omitting some of the options helps to solve it.

Dne středa 24. srpna 2022 v 8:04:21 UTC+2 uživatel Mattia De Vivo napsal: