{"action":"closed","issue":{"url":"https://api.github.com/repos/epruesse/SINA/issues/49","repository_url":"https://api.github.com/repos/epruesse/SINA","labels_url":"https://api.github.com/repos/epruesse/SINA/issues/49/labels{/name}","comments_url":"https://api.github.com/repos/epruesse/SINA/issues/49/comments","events_url":"https://api.github.com/repos/epruesse/SINA/issues/49/events","html_url":"https://github.com/epruesse/SINA/issues/49","id":390216536,"node_id":"MDU6SXNzdWUzOTAyMTY1MzY=","number":49,"title":"align_ident_slv field blank if not 100% identity","user":{"login":"KasperSkytte","id":23030537,"node_id":"MDQ6VXNlcjIzMDMwNTM3","avatar_url":"https://avatars2.githubusercontent.com/u/23030537?v=4","gravatar_id":"","url":"https://api.github.com/users/KasperSkytte","html_url":"https://github.com/KasperSkytte","followers_url":"https://api.github.com/users/KasperSkytte/followers","following_url":"https://api.github.com/users/KasperSkytte/following{/other_user}","gists_url":"https://api.github.com/users/KasperSkytte/gists{/gist_id}","starred_url":"https://api.github.com/users/KasperSkytte/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/KasperSkytte/subscriptions","organizations_url":"https://api.github.com/users/KasperSkytte/orgs","repos_url":"https://api.github.com/users/KasperSkytte/repos","events_url":"https://api.github.com/users/KasperSkytte/events{/privacy}","received_events_url":"https://api.github.com/users/KasperSkytte/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-12-12T13:03:20Z","updated_at":"2018-12-13T11:56:05Z","closed_at":"2018-12-13T11:56:05Z","author_association":"NONE","body":"Hi!\r\n\r\nI have used SINA 1.4.0 to align and assign taxonomy to some full length 16S sequences. When inspecting the output, the field `align_ident_slv` in the output CSV file only shows sequences with an identity of 100, everything else is just blank. I ran the same data on SINA 1.3.5 last week and all fields in the column had a value. This is the command I ran:\r\n\r\n```\r\nsina -i fssu.fa --intype fasta -o output.fa \\\r\n  --meta-fmt csv nearest nuc achieved_idty name \\\r\n  -r refdatabases/SILVA_132_SSURef_NR99_13_12_17_opt.arb --search \\\r\n  --search-db refdatabases/SILVA_132_SSURef_NR99_13_12_17_opt.arb \\\r\n  --lca-fields tax_slv --search-min-sim 0.5 --search-max-result 1 \\\r\n  --num-pts $((THREADS / 2)) --threads $THREADS\r\n```\r\n\r\nI run Ubuntu 18.04 LTS on a Dell 7920 with 40 threads + 128GB RAM. \r\n\r\nThanks in advance\r\nKasper"}}
{"actor":{"display_login":"KasperSkytte"}}