{"action":"created","issue":{"url":"https://api.github.com/repos/marbl/canu/issues/75","repository_url":"https://api.github.com/repos/marbl/canu","labels_url":"https://api.github.com/repos/marbl/canu/issues/75/labels{/name}","comments_url":"https://api.github.com/repos/marbl/canu/issues/75/comments","events_url":"https://api.github.com/repos/marbl/canu/issues/75/events","html_url":"https://github.com/marbl/canu/issues/75","id":142281142,"number":75,"title":"Corrected reads take more time to run than raw reads","user":{"login":"miguelpmachado","id":13034956,"avatar_url":"https://avatars.githubusercontent.com/u/13034956?v=3","gravatar_id":"","url":"https://api.github.com/users/miguelpmachado","html_url":"https://github.com/miguelpmachado","followers_url":"https://api.github.com/users/miguelpmachado/followers","following_url":"https://api.github.com/users/miguelpmachado/following{/other_user}","gists_url":"https://api.github.com/users/miguelpmachado/gists{/gist_id}","starred_url":"https://api.github.com/users/miguelpmachado/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/miguelpmachado/subscriptions","organizations_url":"https://api.github.com/users/miguelpmachado/orgs","repos_url":"https://api.github.com/users/miguelpmachado/repos","events_url":"https://api.github.com/users/miguelpmachado/events{/privacy}","received_events_url":"https://api.github.com/users/miguelpmachado/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2016-03-21T08:07:44Z","updated_at":"2016-03-21T10:50:44Z","closed_at":null,"body":"Hi\r\nIn our lab we have some MiniOn runs, and before I know about CANU I corrected those reads with Nanocorrect and it took around 2 months to correct reads from one run.\r\nAnd now, since I have both corrected and raw reads, I thought of running CANU with both data.\r\nI was expecting that corrected reads take less time to run than raw reads, but it was the other way around:\r\n<code>time canu -p corrected_reads_2 -d ./corrected_reads_2 genomeSize=2.1m maxMemory=10 maxThreads=4 -nanopore-corrected /home/mpmachado/BS313V.200_2d.corrected.fasta)</code>\r\n>real    976m54.460s\r\n>user    3789m23.241s\r\n>sys     1m9.312s\r\n\r\n<code>time canu -p uncorrected_reads_2 -d ./uncorrected_reads_2 genomeSize=2.1m maxMemory=10 maxThreads=4 -nanopore-raw /scratch/mpmachado/minion/GBS313V.200_2d.fasta</code>\r\n>real    463m3.804s\r\n>user    1553m3.544s\r\n>sys     99m10.648s\r\n\r\n`canu --version`\r\n>Canu v1.1 (+18 commits) r7396 91906b6ce56217d765cf1938696ced0e738ca8a3.\r\n\r\nIs this normal? Do you know why is it happens?\r\nThank you in advance.\r\nBest regards,\r\nMiguel"},"comment":{"url":"https://api.github.com/repos/marbl/canu/issues/comments/199223121","html_url":"https://github.com/marbl/canu/issues/75#issuecomment-199223121","issue_url":"https://api.github.com/repos/marbl/canu/issues/75","id":199223121,"user":{"login":"brianwalenz","id":8249720,"avatar_url":"https://avatars.githubusercontent.com/u/8249720?v=3","gravatar_id":"","url":"https://api.github.com/users/brianwalenz","html_url":"https://github.com/brianwalenz","followers_url":"https://api.github.com/users/brianwalenz/followers","following_url":"https://api.github.com/users/brianwalenz/following{/other_user}","gists_url":"https://api.github.com/users/brianwalenz/gists{/gist_id}","starred_url":"https://api.github.com/users/brianwalenz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brianwalenz/subscriptions","organizations_url":"https://api.github.com/users/brianwalenz/orgs","repos_url":"https://api.github.com/users/brianwalenz/repos","events_url":"https://api.github.com/users/brianwalenz/events{/privacy}","received_events_url":"https://api.github.com/users/brianwalenz/received_events","type":"User","site_admin":false},"created_at":"2016-03-21T10:50:44Z","updated_at":"2016-03-21T10:50:44Z","body":"Nice sanity test.\r\n\r\nI'll guess coverage differences.  Canu only corrects the longest 40x (or so) of reads.  Compare the unitigging.html for both.  It doesn't report coverage, but does report number of reads and bases (and not much else at the moment)."}}