{"action":"closed","issue":{"url":"https://api.github.com/repos/PacificBiosciences/Bioinformatics-Training/issues/20","repository_url":"https://api.github.com/repos/PacificBiosciences/Bioinformatics-Training","labels_url":"https://api.github.com/repos/PacificBiosciences/Bioinformatics-Training/issues/20/labels{/name}","comments_url":"https://api.github.com/repos/PacificBiosciences/Bioinformatics-Training/issues/20/comments","events_url":"https://api.github.com/repos/PacificBiosciences/Bioinformatics-Training/issues/20/events","html_url":"https://github.com/PacificBiosciences/Bioinformatics-Training/issues/20","id":111852352,"number":20,"title":"jellyfish memory","user":{"login":"lurebgi","id":5127153,"avatar_url":"https://avatars.githubusercontent.com/u/5127153?v=3","gravatar_id":"","url":"https://api.github.com/users/lurebgi","html_url":"https://github.com/lurebgi","followers_url":"https://api.github.com/users/lurebgi/followers","following_url":"https://api.github.com/users/lurebgi/following{/other_user}","gists_url":"https://api.github.com/users/lurebgi/gists{/gist_id}","starred_url":"https://api.github.com/users/lurebgi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lurebgi/subscriptions","organizations_url":"https://api.github.com/users/lurebgi/orgs","repos_url":"https://api.github.com/users/lurebgi/repos","events_url":"https://api.github.com/users/lurebgi/events{/privacy}","received_events_url":"https://api.github.com/users/lurebgi/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":5,"created_at":"2015-10-16T15:16:04Z","updated_at":"2016-02-17T17:24:29Z","closed_at":"2016-02-17T17:24:29Z","body":"Hi,\r\n\r\nI had 44X bird (genome size 1.2G) pacbio reads, 50G bp in total. My MHAP settings was:\r\nmhap=-k 15 --num-hashes 1024 --num-min-matches 3 --threshold 0.04\r\n\r\nWhen running jellyfish count (-m 15 -s 120000000 -c 6 -t 16), the memory reached 900G before I killed it. Is there any way to reduce the memory usage in kmer count step? Or can I split the fastq files specifically  for jellyfish, then merge the results and continue the rest steps?\r\n\r\nThanks!\r\n\r\nLuohao\r\n\r\n "}}