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hringbauer avatar hringbauer commented on June 17, 2024

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"

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batelz avatar batelz commented on June 17, 2024

The file is there, but it's empty:

(base):~/ancIBD/data/vcf.1240k$ bcftools view example_hazelton_chr22.vcf.gz
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=01/08/2023 - 11:43:29
##source=GLIMPSE_phase v2.0.0
##contig=<ID=chr22>
##INFO=<ID=RAF,Number=A,Type=Float,Description="ALT allele frequency in the reference panel">
##INFO=<ID=AF,Number=A,Type=Float,Description="ALT allele frequency computed from DS/GP field across target samples">
##INFO=<ID=INFO,Number=A,Type=Float,Description="IMPUTE info quality score for diploid samples">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Phased genotypes">
##FORMAT=<ID=GP,Number=3,Type=Float,Description="Genotype posteriors">
##NMAIN=15
##FPLOIDY=2
##bcftools_mergeVersion=1.10.2+htslib-1.10.2-3ubuntu0.1
##bcftools_mergeCommand=merge -l GLIMPSE_ligate/samples_merge.txt -o merged.vcf.gz; Date=Tue Aug  1 13:03:00 2023
##bcftools_annotateVersion=1.10.2+htslib-1.10.2-3ubuntu0.1
##bcftools_annotateCommand=annotate -x ^FORMAT/GT,FORMAT/GP -o GLIMPSE_ligate/merged_chr22_GT_GP.vcf.gz merged.vcf.gz; Date=Tue Aug  1 13:04:43 2023
##bcftools_viewVersion=1.10.2+htslib-1.10.2-3ubuntu0.1
##bcftools_viewCommand=view -Oz -o ./data/vcf.1240k/example_hazelton_chr22.vcf.gz -T ./data/filters/snps_bcftools_ch22.csv -M2 -v snps ./data/vcf.raw/merged_chr22_GT_GP.vcf.gz; Date=Tue Aug  1 13:28:53 2023
##bcftools_viewCommand=view example_hazelton_chr22.vcf.gz; Date=Mon Aug 21 13:20:39 2023
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  S10769.SN       S10770.SN

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hringbauer avatar hringbauer commented on June 17, 2024

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 chr22 notation, but the filter file has 22 only (without the chr). You should transform your VCF accordingly to match the latter notation.

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