{"action":"closed","issue":{"url":"https://api.github.com/repos/samtools/bcftools/issues/892","repository_url":"https://api.github.com/repos/samtools/bcftools","labels_url":"https://api.github.com/repos/samtools/bcftools/issues/892/labels{/name}","comments_url":"https://api.github.com/repos/samtools/bcftools/issues/892/comments","events_url":"https://api.github.com/repos/samtools/bcftools/issues/892/events","html_url":"https://github.com/samtools/bcftools/issues/892","id":364411847,"node_id":"MDU6SXNzdWUzNjQ0MTE4NDc=","number":892,"title":"[E: fai_retrieve] Failed to retrieve block: unexpected end of file. for 23andMe call file","user":{"login":"Ken80","id":43639673,"node_id":"MDQ6VXNlcjQzNjM5Njcz","avatar_url":"https://avatars1.githubusercontent.com/u/43639673?v=4","gravatar_id":"","url":"https://api.github.com/users/Ken80","html_url":"https://github.com/Ken80","followers_url":"https://api.github.com/users/Ken80/followers","following_url":"https://api.github.com/users/Ken80/following{/other_user}","gists_url":"https://api.github.com/users/Ken80/gists{/gist_id}","starred_url":"https://api.github.com/users/Ken80/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Ken80/subscriptions","organizations_url":"https://api.github.com/users/Ken80/orgs","repos_url":"https://api.github.com/users/Ken80/repos","events_url":"https://api.github.com/users/Ken80/events{/privacy}","received_events_url":"https://api.github.com/users/Ken80/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-09-27T10:39:36Z","updated_at":"2018-09-27T11:43:42Z","closed_at":"2018-09-27T11:43:42Z","author_association":"NONE","body":"When I run bcftools convert to try to convert the following 23andMe file from PGP harvard database:\r\nhttps://my.pgp-hms.org/user_file/download/318\r\nto VCF format using the command:\r\nbcftools convert -c ID,CHROM,POS,AA --tsv2vcf GFG7_filtered_unphased_genotypes_23andMe.txt -f /tmp//build37.fa -s /GFG7_filtered_unphased_genotypes_23andMe.txt -Ov -o hu05CA34_3186_GFG7_filtered_unphased_genotypes_23andMe.vcf\r\n\r\nIT crashed straight after the header with the error:\r\n\r\n[E: fai_retrieve] Failed to retrieve block: unexpected end of file.\r\nfaidx_fetch_seq failed at 1:752566\r\n\r\nIt works fine for the other 23andMe txt in this database files but seems to crash on those generated by PLINK\r\n\r\nNot sure if its the tool or the file.\r\n\r\nThanks,\r\nKen\r\n"}}
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