{"action":"closed","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1006","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1006/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1006/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1006/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1006","id":105398153,"number":1006,"title":"Resource request for alignment part of RNASeq workflow does not include samtools","user":{"login":"schelhorn","id":5024959,"avatar_url":"https://avatars.githubusercontent.com/u/5024959?v=3","gravatar_id":"","url":"https://api.github.com/users/schelhorn","html_url":"https://github.com/schelhorn","followers_url":"https://api.github.com/users/schelhorn/followers","following_url":"https://api.github.com/users/schelhorn/following{/other_user}","gists_url":"https://api.github.com/users/schelhorn/gists{/gist_id}","starred_url":"https://api.github.com/users/schelhorn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schelhorn/subscriptions","organizations_url":"https://api.github.com/users/schelhorn/orgs","repos_url":"https://api.github.com/users/schelhorn/repos","events_url":"https://api.github.com/users/schelhorn/events{/privacy}","received_events_url":"https://api.github.com/users/schelhorn/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-09-08T14:47:40Z","updated_at":"2015-09-09T01:33:25Z","closed_at":"2015-09-09T01:33:25Z","body":"I may be mistaken with this, but in the RNASeq pipeline in the alignment section, resources are only specified for the aligner (STAR in my case) and picard:\r\n\r\n```python\r\nwith prun.start(_wres(parallel, [\"aligner\", \"picard\"],\r\n                              ensure_mem={\"tophat\": 8, \"tophat2\": 8, \"star\": 2}),\r\n```\r\n\r\nHowever, when looking at what actually gets executed on the nodes during STAR alignment, it is obvious that STAR [pipes directly into samtools for sorting](https://github.com/chapmanb/bcbio-nextgen/blob/master/bcbio/ngsalign/star.py#L68). However, since the samtools memory is not specified to the parallel environment of the ipython cluster manager in the code shown above, running the workflow may result in terminated jobs if the cluster nodes do not have sufficient memory to also deal with the (unforeseen) samtools part of the pipe."}}