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AlexTISYoung / snipar

Imputation of parental genotypes, inference of sibling IBD segments, family based GWAS, and polygenic score analyses.
MIT License
23 stars 4 forks source link

hap.kin0 not found #14

Closed sjoerdvanalten closed 2 years ago

sjoerdvanalten commented 2 years ago

Hello,

I have installed the package and am trying to familiarize myself with it through the tutorial. However, when running the first line in the tutorial I get an error: 

$python ibd.py example/sample --king example/sample.king.kin0 --agesex example/sample.agesex --map example/sample.genetic_map.txt --outprefix example/ --threads 4

2021-10-18 10:03:26 INFO     start
Traceback (most recent call last):
  File "ibd.py", line 234, in <module>
    kin_header = np.array(open(kinfile,'r').readline().split('\t'))
FileNotFoundError: [Errno 2] No such file or directory: '/disk/genetics4/ukb/alextisyoung/haplotypes/relatives/bedfiles/hap.kin0'

Any idea what could have gone wrong? (testing the packages after installation using pytest went fine I believe)

AlexTISYoung commented 2 years ago

Hi,

Thanks for your email, and apologies for the difficulties you've had. The error in question was caused by an error we made in updating the software with some new developments we had made on IBD inference. This should be solved by updating to the latest version of the software. Please pull the latest version of the master branch with 'git pull origin master' in the SNIPar directory, and reinstall the package.

Let me know if you have any further difficulties.

Thanks,

Alex.

On Mon, 18 Oct 2021 at 03:08, Sjoerd van Alten @.***> wrote:

Hello,

I have installed the package and am trying to familiarize myself with it through the tutorial. However, when running the first line in the tutorial I get an error:

$python ibd.py example/sample --king example/sample.king.kin0 --agesex example/sample.agesex --map example/sample.genetic_map.txt --outprefix example/ --threads 4

2021-10-18 10:03:26 INFO start Traceback (most recent call last): File "ibd.py", line 234, in kin_header = np.array(open(kinfile,'r').readline().split('\t')) FileNotFoundError: [Errno 2] No such file or directory: '/disk/genetics4/ukb/alextisyoung/haplotypes/relatives/bedfiles/hap.kin0'

Any idea what could have gone wrong? (testing the packages after installation using pytest went fine I believe)

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sjoerdvanalten commented 2 years ago

Hi Alex,

Thank you for your quick response. re-installing resolved the issue.

Kind regards, Sjoerd