{"action":"created","issue":{"url":"https://api.github.com/repos/bcgsc/abyss/issues/185","repository_url":"https://api.github.com/repos/bcgsc/abyss","labels_url":"https://api.github.com/repos/bcgsc/abyss/issues/185/labels{/name}","comments_url":"https://api.github.com/repos/bcgsc/abyss/issues/185/comments","events_url":"https://api.github.com/repos/bcgsc/abyss/issues/185/events","html_url":"https://github.com/bcgsc/abyss/issues/185","id":294417851,"number":185,"title":"Running 'ABYSS -k${ksize} -q3 --coverage-hist=coverage.hist -s ${proj}-bubbles.fa in parallel?","user":{"login":"mmokrejs","id":3297852,"avatar_url":"https://avatars1.githubusercontent.com/u/3297852?v=4","gravatar_id":"","url":"https://api.github.com/users/mmokrejs","html_url":"https://github.com/mmokrejs","followers_url":"https://api.github.com/users/mmokrejs/followers","following_url":"https://api.github.com/users/mmokrejs/following{/other_user}","gists_url":"https://api.github.com/users/mmokrejs/gists{/gist_id}","starred_url":"https://api.github.com/users/mmokrejs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mmokrejs/subscriptions","organizations_url":"https://api.github.com/users/mmokrejs/orgs","repos_url":"https://api.github.com/users/mmokrejs/repos","events_url":"https://api.github.com/users/mmokrejs/events{/privacy}","received_events_url":"https://api.github.com/users/mmokrejs/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-02-05T14:46:55Z","updated_at":"2018-02-07T10:54:39Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"Hi,\r\n  I wonder why this is running only in a single thread. I have 2 PE libs and 9 MP files (various levels of confidence of true MP-pairs). Why couldn't abyss act on then in parallel?\r\n\r\n`abyss-pe j=104 k=128 name=... lib='...' mp='...'.`\r\n\r\n I want to run using 104 local threads, no MPI. This is abyss-2.0.2."},"comment":{"url":"https://api.github.com/repos/bcgsc/abyss/issues/comments/363732560","html_url":"https://github.com/bcgsc/abyss/issues/185#issuecomment-363732560","issue_url":"https://api.github.com/repos/bcgsc/abyss/issues/185","id":363732560,"user":{"login":"mmokrejs","id":3297852,"avatar_url":"https://avatars1.githubusercontent.com/u/3297852?v=4","gravatar_id":"","url":"https://api.github.com/users/mmokrejs","html_url":"https://github.com/mmokrejs","followers_url":"https://api.github.com/users/mmokrejs/followers","following_url":"https://api.github.com/users/mmokrejs/following{/other_user}","gists_url":"https://api.github.com/users/mmokrejs/gists{/gist_id}","starred_url":"https://api.github.com/users/mmokrejs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mmokrejs/subscriptions","organizations_url":"https://api.github.com/users/mmokrejs/orgs","repos_url":"https://api.github.com/users/mmokrejs/repos","events_url":"https://api.github.com/users/mmokrejs/events{/privacy}","received_events_url":"https://api.github.com/users/mmokrejs/received_events","type":"User","site_admin":false},"created_at":"2018-02-07T10:54:39Z","updated_at":"2018-02-07T10:54:39Z","author_association":"CONTRIBUTOR","body":"> Unfortunately, no. Genome assembly is not an \"embarassingly parallel\" type of problem where the input files can be split up, processed independently, and then merged.\r\n\r\nBut during k-mer spliting and counting, you could do that in parallel, and then merge the dictionary counters right? It is my impression this \"--coverage-hist\" step is just about this."}}
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