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Merging in LD Map.. results in error #8
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It seems like the output hdf5 file is never produced, and then the last steps (adding map position and allele frequencies to this file) fail because the program cannot find this file. So the error occurs before that - either when producing the 1240k-filtered VCF or the initial output hdf5 file. Is the intermediate 1240k VCF produced? It should be at f"./data/vcf.1240k/example_hazelton_chr{ch}.vcf.gz" |
The file is there, but it's empty:
|
Then I would recommend manually running the bcftools command that creates that intermediary 1240k VCF - and trouble-shoot what goes wrong (nothing matches the SNP filter is the obvious first thing to look into). Indeed, I see from the above that you have |
Hi again.
This issue can be merged with #5.
I've used GLIMPSE to impute two samples, and resulted with the following vcf file:
When trying to convert to HD5 using
I get the following error:
The directory does exist, as I get no error when running:
os.listdir("./data/hdf5/")
and I've also tried writing the absolute path.
Moreover, when running the example you provided -- just by switching the
in_vcf
it runs perfectly fine.So it must be something in the vcf file iteslf.
Any ideas?
Batel
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