{"action":"created","issue":{"url":"https://api.github.com/repos/marbl/canu/issues/672","repository_url":"https://api.github.com/repos/marbl/canu","labels_url":"https://api.github.com/repos/marbl/canu/issues/672/labels{/name}","comments_url":"https://api.github.com/repos/marbl/canu/issues/672/comments","events_url":"https://api.github.com/repos/marbl/canu/issues/672/events","html_url":"https://github.com/marbl/canu/issues/672","id":265864547,"number":672,"title":"qsub, -t option","user":{"login":"TonyMane","id":32308413,"avatar_url":"https://avatars1.githubusercontent.com/u/32308413?v=4","gravatar_id":"","url":"https://api.github.com/users/TonyMane","html_url":"https://github.com/TonyMane","followers_url":"https://api.github.com/users/TonyMane/followers","following_url":"https://api.github.com/users/TonyMane/following{/other_user}","gists_url":"https://api.github.com/users/TonyMane/gists{/gist_id}","starred_url":"https://api.github.com/users/TonyMane/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/TonyMane/subscriptions","organizations_url":"https://api.github.com/users/TonyMane/orgs","repos_url":"https://api.github.com/users/TonyMane/repos","events_url":"https://api.github.com/users/TonyMane/events{/privacy}","received_events_url":"https://api.github.com/users/TonyMane/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2017-10-16T18:14:14Z","updated_at":"2017-10-20T15:18:44Z","closed_at":null,"author_association":"NONE","body":"Greetings, I am using Canu 1.6, on  a grid (PBS). I am trying to assemble a metagenome. I am not entirely sure if this is a canu specific question, or a question that requires some insight into PBS job submission. Regardless, i continually receive a qsub submission error during the assembly process in the file 'red.jobSubmit-02.out' located in the unitigging/unitigging/3-overlapErrorAdjustment/..\r\n\r\n'qsub: submit error (Maximum number of jobs already in queue MSG=Job 3382993.dedicated-sched.pace.gatech.edu violates the global server limit of 3000 jobs queued per user)'\r\n\r\nSo, i added 'gridEngineArrayMaxJobs=2000' to the pbs script, and then continued the canu pipeline, but started at the assembly stage. it looks like the same process was encountered, I did notice that that the error was in 'red.jobSubmit-03.out'. Also, I noticed in the 'canu.out' file, that there were two separate files started:\r\n```\r\n'-- 'red.jobSubmit-01.sh' -> job 3386904[].dedicated-sched.pace.gatech.edu tasks 1-2000.\r\n-- 'red.jobSubmit-02.sh' -> job 3386905[].dedicated-sched.pace.gatech.edu tasks 2001-4000.\r\n\r\nCRASH:\r\nCRASH: Canu snapshot v1.6 +61 changes (r8473 86f53cff1401ce4229d2a579ed093afe68751e0a)\r\nCRASH: Please panic, this is abnormal.I was under the impression that the -t option provided a maximum number of submissions, that were then distributed equally.'\r\n```\r\nI am wondering if anyone has had a similar issue, and which parameter they modified. \r\n\r\nthanks!"},"comment":{"url":"https://api.github.com/repos/marbl/canu/issues/comments/338237094","html_url":"https://github.com/marbl/canu/issues/672#issuecomment-338237094","issue_url":"https://api.github.com/repos/marbl/canu/issues/672","id":338237094,"user":{"login":"TonyMane","id":32308413,"avatar_url":"https://avatars1.githubusercontent.com/u/32308413?v=4","gravatar_id":"","url":"https://api.github.com/users/TonyMane","html_url":"https://github.com/TonyMane","followers_url":"https://api.github.com/users/TonyMane/followers","following_url":"https://api.github.com/users/TonyMane/following{/other_user}","gists_url":"https://api.github.com/users/TonyMane/gists{/gist_id}","starred_url":"https://api.github.com/users/TonyMane/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/TonyMane/subscriptions","organizations_url":"https://api.github.com/users/TonyMane/orgs","repos_url":"https://api.github.com/users/TonyMane/repos","events_url":"https://api.github.com/users/TonyMane/events{/privacy}","received_events_url":"https://api.github.com/users/TonyMane/received_events","type":"User","site_admin":false},"created_at":"2017-10-20T15:18:44Z","updated_at":"2017-10-20T15:18:44Z","author_association":"NONE","body":"thanks for the support. a few more questions. the 'tip' version will print the below statement when supplied with the version;\r\n`/nv/hp10/abertagnolli3/scratch/data/canu/Linux-amd64/bin/canu -version\r\nCanu snapshot v1.6 +61 changes (r8473 86f53cff1401ce4229d2a579ed093afe68751e0a)`\r\n\r\nand the stable version, or the version you would suggest using will look like this:\r\n\r\n`/nv/hp10/abertagnolli3/scratch/data/canu-master/Linux-amd64/bin/canu -version\r\nCanu 1.6`\r\n\r\nis that correct? \r\n\r\nSecond, we started the pipeline from scratch, using i what i think is the tip version. i believe now it is having a memory issue with mmap. can we increase this 'mmapMemory=5g'? I have attached the output of the first 'precompute.1.out-1 ' (there were 9 total, all with similar outputs, the amount of memory being listing being different for all 9). \r\n\r\nthanks for you for your support!\r\n\r\n[canu_metagenome_mostRecent.pbs.txt](https://github.com/marbl/canu/files/1402422/canu_metagenome_mostRecent.pbs.txt)\r\n\r\n[precompute.1.out-1.txt](https://github.com/marbl/canu/files/1402421/precompute.1.out-1.txt)\r\n\r\n \r\n\r\n"}}
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