{"action":"created","issue":{"url":"https://api.github.com/repos/FelixKrueger/Bismark/issues/106","repository_url":"https://api.github.com/repos/FelixKrueger/Bismark","labels_url":"https://api.github.com/repos/FelixKrueger/Bismark/issues/106/labels{/name}","comments_url":"https://api.github.com/repos/FelixKrueger/Bismark/issues/106/comments","events_url":"https://api.github.com/repos/FelixKrueger/Bismark/issues/106/events","html_url":"https://github.com/FelixKrueger/Bismark/issues/106","id":228071938,"number":106,"title":"Extremely slow bismark bisulfite mapping using bowtie2 and --score_min","user":{"login":"sansense","id":2727717,"avatar_url":"https://avatars0.githubusercontent.com/u/2727717?v=3","gravatar_id":"","url":"https://api.github.com/users/sansense","html_url":"https://github.com/sansense","followers_url":"https://api.github.com/users/sansense/followers","following_url":"https://api.github.com/users/sansense/following{/other_user}","gists_url":"https://api.github.com/users/sansense/gists{/gist_id}","starred_url":"https://api.github.com/users/sansense/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sansense/subscriptions","organizations_url":"https://api.github.com/users/sansense/orgs","repos_url":"https://api.github.com/users/sansense/repos","events_url":"https://api.github.com/users/sansense/events{/privacy}","received_events_url":"https://api.github.com/users/sansense/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":14,"created_at":"2017-05-11T17:52:50Z","updated_at":"2017-06-07T11:46:32Z","closed_at":null,"body":"I am trying to map paired-end reads from an amplicon sequencing using Bismark. The command line is \r\n\r\n    bismark --un --ambiguous --maxins 1000 --non_directional --score_min L,-0.6,-1 bismark-genome-folder -1 R1.fastq.gz -2 R2.fastq.gz\r\n\r\nThis is running extremely slow @ around 50000 reads / hour / thread (an estimate from bam-file). I've checked the mapping on three different machines having different specs using: 1) single thread 2) 4 threads and 3) 10 threads. The reaultant speed I'm getting is similar.\r\n\r\nI had run the same mapping in single end mode in past (for R1 and R2 separately) and it ran at a reasonable speed. I don't remember the exact speed but at least it was finished in 1-2 days, whereas I'm still waiting for the results of mapping after 3 days (single thread) or 1 day (10 threads). \r\n\r\nNext, I did a quick check to see the differences in time by using first 1000 reads of the same (as above) sample\r\n\r\n**single-end**\r\n\r\n    time bismark --un --ambiguous --non_directional --score_min L,-0.6,-1 bismark-genome-folder  1kr1.fq\r\n    \r\n    real\t0m7.883s\r\n    user\t0m2.523s\r\n    sys\t0m0.101s\r\n    \r\n    \r\n**paired-end**\r\n\r\n    time bismark --un --ambiguous --non_directional --score_min L,-0.6,-1  bismark-genome-folder  -1 1kr1.fq -2 1kr2.fq\r\n    \r\n    real\t1m25.260s\r\n    user\t0m8.001s\r\n    sys\t0m0.141s\r\n\r\n**This suggests that paired-end mapping is running at least 10 times slower!** Has anyone faced similar issues? How to make the mapping faster?\r\n\r\n*Finer Details:* \r\nMy reference sequences (total ~250) are almost the same (excluding difference of around 30-40 bp in the middle of sequences), length around 800bp each. 150bp, untrimmed reads.  \r\n\r\nPS: Cross posted on Biostars https://www.biostars.org/p/252276/"},"comment":{"url":"https://api.github.com/repos/FelixKrueger/Bismark/issues/comments/306770615","html_url":"https://github.com/FelixKrueger/Bismark/issues/106#issuecomment-306770615","issue_url":"https://api.github.com/repos/FelixKrueger/Bismark/issues/106","id":306770615,"user":{"login":"sansense","id":2727717,"avatar_url":"https://avatars0.githubusercontent.com/u/2727717?v=3","gravatar_id":"","url":"https://api.github.com/users/sansense","html_url":"https://github.com/sansense","followers_url":"https://api.github.com/users/sansense/followers","following_url":"https://api.github.com/users/sansense/following{/other_user}","gists_url":"https://api.github.com/users/sansense/gists{/gist_id}","starred_url":"https://api.github.com/users/sansense/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sansense/subscriptions","organizations_url":"https://api.github.com/users/sansense/orgs","repos_url":"https://api.github.com/users/sansense/repos","events_url":"https://api.github.com/users/sansense/events{/privacy}","received_events_url":"https://api.github.com/users/sansense/received_events","type":"User","site_admin":false},"created_at":"2017-06-07T11:46:32Z","updated_at":"2017-06-07T11:46:32Z","body":"My question was about the extraction time, that seems to be pretty slow. So a full extractions (CpG + Non_CpG) will take almost half day. Is that usual?"}}
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