{"action":"created","issue":{"url":"https://api.github.com/repos/faircloth-lab/phyluce/issues/76","repository_url":"https://api.github.com/repos/faircloth-lab/phyluce","labels_url":"https://api.github.com/repos/faircloth-lab/phyluce/issues/76/labels{/name}","comments_url":"https://api.github.com/repos/faircloth-lab/phyluce/issues/76/comments","events_url":"https://api.github.com/repos/faircloth-lab/phyluce/issues/76/events","html_url":"https://github.com/faircloth-lab/phyluce/issues/76","id":243872058,"number":76,"title":"Running individual assemblies","user":{"login":"leonvarhan","id":25911288,"avatar_url":"https://avatars3.githubusercontent.com/u/25911288?v=4","gravatar_id":"","url":"https://api.github.com/users/leonvarhan","html_url":"https://github.com/leonvarhan","followers_url":"https://api.github.com/users/leonvarhan/followers","following_url":"https://api.github.com/users/leonvarhan/following{/other_user}","gists_url":"https://api.github.com/users/leonvarhan/gists{/gist_id}","starred_url":"https://api.github.com/users/leonvarhan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/leonvarhan/subscriptions","organizations_url":"https://api.github.com/users/leonvarhan/orgs","repos_url":"https://api.github.com/users/leonvarhan/repos","events_url":"https://api.github.com/users/leonvarhan/events{/privacy}","received_events_url":"https://api.github.com/users/leonvarhan/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-07-18T22:39:10Z","updated_at":"2017-07-19T13:13:31Z","closed_at":null,"body":"Hello, \r\nI am trying to run my data assembly in an HPC, but it is taking too long to get started and the job gets killed due to not enough memory or not enough time. I was wondering if I could run each species separately creating individual \"assembly.conf\" files.  Will there be any conflict if I run the \"phyluce_assembly_assemblo_trinity\" program for all 50 species simultaneously ??? Will it generate 50 separate \"phyluce_assembly_assemblo_trinity.log\" files???\r\nfor example:\r\nphyluce_assembly_assemblo_trinity \\\r\n        --conf assembly_species_01.conf \\\r\n        --output trinity_assemblies_species01 \\\r\n        --subfolder split-adapter-quality-trimmed \\\r\n        --clean \\\r\n        --cores 28\r\nphyluce_assembly_assemblo_trinity \\\r\n        --conf assembly_species_02.conf \\\r\n        --output trinity_assemblies_species02 \\\r\n        --subfolder split-adapter-quality-trimmed \\\r\n        --clean \\\r\n        --cores 28\r\n…\r\netc\r\nThank you for your time, \r\nLV. \r\n"},"comment":{"url":"https://api.github.com/repos/faircloth-lab/phyluce/issues/comments/316381868","html_url":"https://github.com/faircloth-lab/phyluce/issues/76#issuecomment-316381868","issue_url":"https://api.github.com/repos/faircloth-lab/phyluce/issues/76","id":316381868,"user":{"login":"brantfaircloth","id":54026,"avatar_url":"https://avatars0.githubusercontent.com/u/54026?v=4","gravatar_id":"","url":"https://api.github.com/users/brantfaircloth","html_url":"https://github.com/brantfaircloth","followers_url":"https://api.github.com/users/brantfaircloth/followers","following_url":"https://api.github.com/users/brantfaircloth/following{/other_user}","gists_url":"https://api.github.com/users/brantfaircloth/gists{/gist_id}","starred_url":"https://api.github.com/users/brantfaircloth/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brantfaircloth/subscriptions","organizations_url":"https://api.github.com/users/brantfaircloth/orgs","repos_url":"https://api.github.com/users/brantfaircloth/repos","events_url":"https://api.github.com/users/brantfaircloth/events{/privacy}","received_events_url":"https://api.github.com/users/brantfaircloth/received_events","type":"User","site_admin":false},"created_at":"2017-07-19T13:13:31Z","updated_at":"2017-07-19T13:13:31Z","body":"Yes, you could generate many `assembly.conf` files and just submit each as an individual job.  Mike's suggestion is also a good one (using a particular script for HPC).  On our HPC, we use GNU parallel to sometimes run the Trinity assemblies.  You can also try to use the `--dir` option instead of the `--conf` option - the former simply takes a directory full of reads and created an output folder holding the assemblies.\r\n\r\nWhat you will find, depending on how you go about it, is that you may need to create your own `contigs` folder where all the assemblies from each individual run are symlinked, so you get something like:\r\n```\r\nmy_symlink.contigs.fasta -> /path/to/my/individual/assembly/Trinity.fasta\r\n```\r\nThis is basically one thing that `phyluce_assembly_assemblo_trinity` doing.  You'll also have to deal with cleaning up intermediate files, which often cause problems on HPC systems."}}
{"actor":{"display_login":"brantfaircloth"}}