AssertionError: Sample ploidy (2) doesn't match number of sequences (3) about genomics_general

[simonhmartin]

Sorry for the delay. I'm not sure what the problem is, but I suspect it might be something odd about teh way your genotypes are encoded. Are you sure all genotypes are single nucleotides (like "A/T") and not indels (like "A/TAA")?

[fushike]

Hi Simon,
I checked the genotypes of my samples and didn't find any individuals with indels.
Here is an example of the genotype data
NewChr10 255917 A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/T A/A A/A A/A A/A A/T A/A A/A A/A A/T N/N A/A A/A A/A A/A A/A A/A N/N A/A A/T A/A A/A A/A A/T A/A N/N A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A N/N A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/A A/T N/N A/T A/A

[simonhmartin]

Hi Fushi,
This is a puzzle. The only thing I can recommend is to make reduced versions of your geno file with say 1000 lines, 2000 lines etc, to try to find out which line in particular is causing the script to fail.

[rafmarcondes]

Hi Fushi and Simon,

Did you end up finding a solution for this? I'm encountering the same error. I converted my vcf to geno using parseVCF.py --skipIndels.

Here's my command:

python /home/rmarco3/bin/simon-martin-scripts/popgenWindows.py -T 4 -g asp_con_din_par_quality_filtered_ONLY.geno --windType coordinate -w 50000 -s 25000 --popsFile pops_file_for_martin -p asp -p par -f pairs --verbose -o simon_stats_aspVpar

Thanks for any help!

[fushike]

Hi Rafael, I am not sure if it will work in your system, but I remove the -f pairs command and find it works well. hope it will help, Best Fushi From: Rafael Marcondes Date: 2020-07-11 03:16 To: simonhmartin/genomics_general CC: fushike; Author Subject: Re: [simonhmartin/genomics_general] AssertionError: Sample ploidy (2) doesn't match number of sequences (3) (#18) Hi Fushi and Simon, Did you end up finding a solution for this? I'm encountering the same error. I converted my vcf to geno using parseVCF.py --skipIndels. Here's my command: python /home/rmarco3/bin/simon-martin-scripts/popgenWindows.py -T 4 -g asp_con_din_par_quality_filtered_ONLY.geno --windType coordinate -w 50000 -s 25000 --popsFile pops_file_for_martin -p asp -p par -f pairs --verbose -o simon_stats_aspVpar Thanks for any help! — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

[fushike]

Hi Fushi and Simon,

Did you end up finding a solution for this? I'm encountering the same error. I converted my vcf to geno using parseVCF.py --skipIndels.

Here's my command:

python /home/rmarco3/bin/simon-martin-scripts/popgenWindows.py -T 4 -g asp_con_din_par_quality_filtered_ONLY.geno --windType coordinate -w 50000 -s 25000 --popsFile pops_file_for_martin -p asp -p par -f pairs --verbose -o simon_stats_aspVpar

Thanks for any help!

Hi Rafael,

In the README.md file, you can find -f pairs refers to genotype without a line between alleles. And "-f phased", should be proper in the situation with or without phasing.

• Genotypes can be incoded in various ways, as indicated by the -f flag.
  -f phased means that genotypes include phase information (but they don't necessarily need to actually be phased):

scaffold1  1        A/A       G/G       G|A

-f pairs is the same, but without the phase indicator:

scaffold1  1        AA       GG       AG

-f haplo means that genotypes are haploid bases:

scaffold1  1        A       G       G

-f diplo means that genotypes are single bases denoting the diploid genotype, using ambiguity codes for heterozygotes:

scaffold1  1        A       G       R


Best,

Fushi

[rafmarcondes]

Thanks, Fushi. Yea, it's working now with -f phased.