{"action":"created","issue":{"url":"https://api.github.com/repos/FofanovLab/MTSv/issues/3","repository_url":"https://api.github.com/repos/FofanovLab/MTSv","labels_url":"https://api.github.com/repos/FofanovLab/MTSv/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/FofanovLab/MTSv/issues/3/comments","events_url":"https://api.github.com/repos/FofanovLab/MTSv/issues/3/events","html_url":"https://github.com/FofanovLab/MTSv/issues/3","id":317741665,"number":3,"title":"MTSv-summary lacks graceful exit","user":{"login":"vyfofanov","id":1382818,"avatar_url":"https://avatars2.githubusercontent.com/u/1382818?v=4","gravatar_id":"","url":"https://api.github.com/users/vyfofanov","html_url":"https://github.com/vyfofanov","followers_url":"https://api.github.com/users/vyfofanov/followers","following_url":"https://api.github.com/users/vyfofanov/following{/other_user}","gists_url":"https://api.github.com/users/vyfofanov/gists{/gist_id}","starred_url":"https://api.github.com/users/vyfofanov/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vyfofanov/subscriptions","organizations_url":"https://api.github.com/users/vyfofanov/orgs","repos_url":"https://api.github.com/users/vyfofanov/repos","events_url":"https://api.github.com/users/vyfofanov/events{/privacy}","received_events_url":"https://api.github.com/users/vyfofanov/received_events","type":"User","site_admin":false},"labels":[{"id":779017580,"url":"https://api.github.com/repos/FofanovLab/MTSv/labels/bug","name":"bug","color":"ee0701","default":true}],"state":"open","locked":false,"assignee":{"login":"tfursten","id":4183685,"avatar_url":"https://avatars3.githubusercontent.com/u/4183685?v=4","gravatar_id":"","url":"https://api.github.com/users/tfursten","html_url":"https://github.com/tfursten","followers_url":"https://api.github.com/users/tfursten/followers","following_url":"https://api.github.com/users/tfursten/following{/other_user}","gists_url":"https://api.github.com/users/tfursten/gists{/gist_id}","starred_url":"https://api.github.com/users/tfursten/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tfursten/subscriptions","organizations_url":"https://api.github.com/users/tfursten/orgs","repos_url":"https://api.github.com/users/tfursten/repos","events_url":"https://api.github.com/users/tfursten/events{/privacy}","received_events_url":"https://api.github.com/users/tfursten/received_events","type":"User","site_admin":false},"assignees":[{"login":"tfursten","id":4183685,"avatar_url":"https://avatars3.githubusercontent.com/u/4183685?v=4","gravatar_id":"","url":"https://api.github.com/users/tfursten","html_url":"https://github.com/tfursten","followers_url":"https://api.github.com/users/tfursten/followers","following_url":"https://api.github.com/users/tfursten/following{/other_user}","gists_url":"https://api.github.com/users/tfursten/gists{/gist_id}","starred_url":"https://api.github.com/users/tfursten/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tfursten/subscriptions","organizations_url":"https://api.github.com/users/tfursten/orgs","repos_url":"https://api.github.com/users/tfursten/repos","events_url":"https://api.github.com/users/tfursten/events{/privacy}","received_events_url":"https://api.github.com/users/tfursten/received_events","type":"User","site_admin":false},{"login":"ktaed","id":10564357,"avatar_url":"https://avatars1.githubusercontent.com/u/10564357?v=4","gravatar_id":"","url":"https://api.github.com/users/ktaed","html_url":"https://github.com/ktaed","followers_url":"https://api.github.com/users/ktaed/followers","following_url":"https://api.github.com/users/ktaed/following{/other_user}","gists_url":"https://api.github.com/users/ktaed/gists{/gist_id}","starred_url":"https://api.github.com/users/ktaed/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ktaed/subscriptions","organizations_url":"https://api.github.com/users/ktaed/orgs","repos_url":"https://api.github.com/users/ktaed/repos","events_url":"https://api.github.com/users/ktaed/events{/privacy}","received_events_url":"https://api.github.com/users/ktaed/received_events","type":"User","site_admin":false}],"milestone":null,"comments":0,"created_at":"2018-04-25T18:24:01Z","updated_at":"2018-04-25T23:52:51Z","closed_at":null,"author_association":"NONE","body":"MTSv-summary.py crashes (see below for traceback message) when it encounters a taxID that is not in it's database.  This is going to happen more often once we start adding custom DBs from chromosome and scaffold portion of NCBI (which may be updated at a different rate than the original GenBank).\r\n\r\nRather than throwing an exception and crashing we should put such reads into 'unknown' category and report them.  Note that when we are not running \"--lca 0\" option and are instead using genus or family option, we'll need to assume that all unknown hits are non-signatures to be safe.\r\n\r\nTo replicate on monsoon, use the following collapsed, signature, and taxdump files respectively:\r\n\r\n- /scratch/vyf2/CR2/metaSlava/bats/vedro/NHCS-EchoLake01.clp\r\n- /scratch/vyf2/CR2/metaSlava/bats/vedro/NHCS-EchoLake01.sig\r\n- /scratch/vyf2/NCBI_012417/treeBuild/taxdump.tar.gz\r\n\r\n\r\n\r\n==\r\nTraceback (most recent call last):\r\n  File \"/home/vyf2/MTSv/scripts/MTSv_summary.py\", line 234, in <module>\r\n    get_summary(ARGS.all, ARGS.sig, outfile, ARGS.threads, ARGS.verbose)\r\n  File \"/home/vyf2/MTSv/scripts/MTSv_summary.py\", line 152, in get_summary\r\n    row_list = [taxa, tax2div(taxa), taxid2name[taxa]]\r\n  File \"/home/vyf2/MTSv/scripts/MTSv_summary.py\", line 42, in tax2div\r\n    lineage = NCBI.get_lineage(taxid)\r\n  File \"/home/vyf2/.conda/envs/biopy3/lib/python3.5/site-packages/ete3/ncbi_taxonomy/ncbiquery.py\", line 238, in get_lineage\r\n    raise ValueError(\"%s taxid not found\" %taxid)\r\nValueError: 1526222 taxid not found\r\n"},"comment":{"url":"https://api.github.com/repos/FofanovLab/MTSv/issues/comments/384469048","html_url":"https://github.com/FofanovLab/MTSv/issues/3#issuecomment-384469048","issue_url":"https://api.github.com/repos/FofanovLab/MTSv/issues/3","id":384469048,"user":{"login":"tfursten","id":4183685,"avatar_url":"https://avatars3.githubusercontent.com/u/4183685?v=4","gravatar_id":"","url":"https://api.github.com/users/tfursten","html_url":"https://github.com/tfursten","followers_url":"https://api.github.com/users/tfursten/followers","following_url":"https://api.github.com/users/tfursten/following{/other_user}","gists_url":"https://api.github.com/users/tfursten/gists{/gist_id}","starred_url":"https://api.github.com/users/tfursten/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/tfursten/subscriptions","organizations_url":"https://api.github.com/users/tfursten/orgs","repos_url":"https://api.github.com/users/tfursten/repos","events_url":"https://api.github.com/users/tfursten/events{/privacy}","received_events_url":"https://api.github.com/users/tfursten/received_events","type":"User","site_admin":false},"created_at":"2018-04-25T23:52:51Z","updated_at":"2018-04-25T23:52:51Z","author_association":"OWNER","body":"This should be fixed with latest commit. I was able to produce the summary file at /scratch/tf362/for_slava/Bats_summary.csv"}}
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