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DReichLab / EIG

Eigen tools by Nick Patterson and Alkes Price lab
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genotype file bad line #73

Closed DcornishUCL closed 3 years ago

DcornishUCL commented 3 years ago

Hi,

I have been trying to perform mergeit and I am receiving the error below:

fatalx: file.geno bad line: 92992229999999999929992999992229992299999929299992

I checked whether the number of characters in each line == number of individuals and indeed lines have the expected 50 individuals suggesting the error is not caused by missing individuals. I did the same with the number of SNPs and all is as expected. Any help you could offer to help me rectify this problem would be much appreciated. I attach a few lines of the offending .geno file below in case this helps.

Best,

Dean

geno.file:

92992229999999999929992999992229992299999929299992 92992229999999999929992999992229992299999929299992 90999229999999999929992999992229992299999929299992 22299229999929999222999992929929999999999229922992 29299229999999999929999999922229929929999929292999 22222229999929929929992992922229929929999229222929 22222229999929929929992992922229929929999229222922 22222229999222929929992992922229929929999229222922 22222229999222929929992992922229929929999229222922

bumblenick commented 3 years ago
  1. Please check that your param file doesn't have some error (like specifying an ind file as a geno file
  2. Check that the geno file doesn't have strange characters like tabs.

This is some input blunder with probability .999999 For further correspondence please email me direct: < @.***>

Nick

On Thu, Nov 4, 2021 at 9:00 AM Dean Cornish @.***> wrote:

Hi,

I have been trying to perform mergeit and I am receiving the error below:

fatalx: file.geno bad line: 92992229999999999929992999992229992299999929299992

I checked whether the number of characters in each line == number of individuals and indeed lines have the expected 50 individuals suggesting the error is not caused by missing individuals. I did the same with the number of SNPs and all is as expected. Any help you could offer to help me rectify this problem would be much appreciated. I attach a few lines of the offending .geno .snp and .ind files converted to txt below in case this helps.

Best,

Dean

geno.file:

92992229999999999929992999992229992299999929299992 92992229999999999929992999992229992299999929299992 90999229999999999929992999992229992299999929299992 22299229999929999222999992929929999999999229922992 29299229999999999929999999922229929929999929292999 22222229999929929929992992922229929929999229222929 22222229999929929929992992922229929929999229222922 22222229999222929929992992922229929929999229222922 22222229999222929929992992922229929929999229222922

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DcornishUCL commented 3 years ago

Hi,

Yes, I spotted it! I had mistakenly specified the ind as the geno file. My apologies, thank you for alerting me to this.