Error when using populations -aborted(core dumped)

[bluemo...@gmail.com]

Hi,

I am a stacks newbie and am having issues when I try to run populations. Its running on linux ubuntu from a vcf file generated from a different software. Here is my command:

populations -V ./g5ind60.recode.vcf -M ./Pop_map.txt -O ./het -p 1 -r 0.75 --min_maf 0.03 --max-obs-het 0.8 --vcf --structure --genepop
 

it starts running but then aborts. The last few sections in the terminal are the following:

SNPs and calls will be written in VCF format to './het/g5ind60.recode.p.snps.vcf'
Haplotypes will be written in VCF format to './het/g5ind60.recode.p.haps.vcf'
Polymorphic sites in Structure format will be written to './het/g5ind60.recode.p.structure'
Polymorphic sites in GenePop format will be written to './het/g5ind60.recode.p.snps.genepop'
Warning: Genepop: The order in which samples appear was modified (as the input population map is not sorted).Polymorphic loci in GenePop format will be written to './het/g5ind60.recode.p.haps.genepop'
Genotyping markers will be written to './het/g5ind60.recode.p.markers.tsv'
Raw Genotypes/Haplotypes will be written to './het/g5ind60.recode.p.haplotypes.tsv'
Population-level summary statistics will be written to './het/g5ind60.recode.p.sumstats.tsv'
Population-level haplotype summary statistics will be written to './het/g5ind60.recode.p.hapstats.tsv'

Processing data in batches:
  * load a batch of catalog loci and apply filters
  * compute SNP- and haplotype-wise per-population statistics
  * write the above statistics in the output files
  * export the genotypes/haplotypes in specified format(s)
More details in './het/g5ind60.recode.p.log.distribs'.
Now processing...
locus_544 populations: src/export_formats.cc:2169: virtual int VcfExport::write_site(const CSLocus*, const LocPopSum*, const Datum* const*, std::size_t, std::size_t): Assertion `d[s]->snpdata[index].gq != UINT8_MAX' failed.

I looked through other posts and didn't see anything similar with an abort message specifying a specific locus. Could there be a format issue with my vcf file?

Thanks in advance!

Alanna

[Francisco Sepúlveda Espinoza]

Hi!

I' m having a similar issue.

I have a vcf file obtained from ipyrad, and I want to run population on stack to apply some filters: 

> populations -V ./Ipyrad_PE_T1.vcf -M ./Popmap_PE_IPYRAD.txt -O ./ -r 0.5 --write-single-snp --vcf

and the program starts running but failed: 

Parsing population map...

The population map contained 89 samples, 5 population(s), 1 group(s).

Opening the VCF file...

Working on 89 samples.

Working on 5 population(s):

    VerdeII: 1, 12, 13, 20, 25, 3

    Rojo: 109, 109b, 112, 126, 128, 138, 143, 149, 149b, 151, 161, 166, 167, 170, 181, 79, 82, 91, 91b, 92

    Azul: 145, 147, 183, 195, 198, 199, 209, 211, 211b, 217, 222, 222b, 224, 227, 230, 232, 240, 240b, 252, 257, 267, 268, 272, 276,

          277, 280, 282, 300, 364, 368, 371, 378, 382, 387, 387b, 393, 396, 410, 416, 417, 62, 68, 76, 93, 98

    VerdeI: 30, 37, 39, 41, 420, 424, 425, 432, 44, 445, 456, 46

    Amarillo: 311, 316, 323, 334, 341, 346

Working on 1 group(s) of populations:

    defaultgrp: VerdeII, Rojo, Azul, VerdeI, Amarillo

SNPs and calls will be written in VCF format to './Ipyrad_PE_T1.p.snps.vcf'

Raw haplotypes will be written to './Ipyrad_PE_T1.p.haplotypes.tsv'

Population-level summary statistics will be written to './Ipyrad_PE_T1.p.sumstats.tsv'

Population-level haplotype summary statistics will be written to './Ipyrad_PE_T1.p.hapstats.tsv'

Processing data in batches:

  * load a batch of catalog loci and apply filters

  * compute SNP- and haplotype-wise per-population statistics

  * write the above statistics in the output files

  * export the genotypes/haplotypes in specified format(s)

More details in './Ipyrad_PE_T1.p.log.distribs'.

Now processing...

RAD_0 populations: src/utils.h:121: double GtLiks::at(std::size_t) const: Assertion `has_lik(gt)' failed.

Aborted (core dumped)

 someone resolve it?

thanks!

[Tanya Lama]

Hi Fransisco, I'm experiencing a similar issue with populations. 

Is there any information on the following error: 

NC_044303.1 populations: src/utils.h:120: double GtLiks::at(std::size_t) const: Assertion `has_lik(gt)' failed.

Aborted

Thanks

[Francisco Sepúlveda Espinoza]

Hi Tanya!

I read some old posts from Julian and he says that VCF from Ipyrad has different information from that created from STACKs. I can't find it right now, but I'm looking for it. 

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Francisco Sepúlveda Espinoza

Ingeniero en Biotecnología Vegetal

M.Sc(c) mención Genética - Universidad Austral de Chile

[Tanya Lama]

Oh dear. What was your solution? My VCF is actually from GATK, not ipyrad. I am starting to think it's not compatible with the stacks populations module and am exploring other ways of calculating pairwise Φst

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Tanya Lama
PhD Candidate
Massachusetts Cooperative Fish & Wildlife Research Unit
University of Massachusetts Amherst

160 Holdsworth Way

Amherst, MA 01003

(203) 824-9286

[Francisco Sepúlveda Espinoza]

What about R? Fstamp or hierfstats are really good packages to do it. 

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[Miranda Sherlock]

Hi all,

I'm having a similar issue with a dDocent VCF (I need to group some populations and re-make the VCF to make a SFS for fastsimcoal2).

Now processing...

dDocent_Contig_1 Assertion failed: (d[s]->snpdata[index].gq != UINT8_MAX), function write_site, file export_formats.cc, line 2663.

zsh: abort      ./populations -V  --vcf -M  -O 

Has anyone found a solution to this?

Thanks,

Miranda

[Catchen, Julian]

Hi Miranda,

 

The error is saying that the genotype quality (GQ) field of the dDocent VCF is not an integer (whole, counting number), as required by the VCF standard (it is likely blank). You may be able to find and remove that line from your VCF, but hard to say. You should also make sure you are on the latest Stacks release, as we have made a few VCF fixes recently. The simplest solution is to run your data through Stacks proper to get the VCF export.

 

julian

[Miranda Sherlock]

Hi Julian,

Thanks for answering. I checked the VCF and indeed the GQ field values were not integers (many are), I got round this by removing individuals using VCFtools.

Miranda