{"action":"closed","issue":{"url":"https://api.github.com/repos/deweylab/RSEM/issues/14","labels_url":"https://api.github.com/repos/deweylab/RSEM/issues/14/labels{/name}","comments_url":"https://api.github.com/repos/deweylab/RSEM/issues/14/comments","events_url":"https://api.github.com/repos/deweylab/RSEM/issues/14/events","html_url":"https://github.com/deweylab/RSEM/issues/14","id":93626731,"number":14,"title":"rsem-calculate-expression error ","user":{"login":"qwangmsk","id":11812514,"avatar_url":"https://avatars.githubusercontent.com/u/11812514?v=3","gravatar_id":"","url":"https://api.github.com/users/qwangmsk","html_url":"https://github.com/qwangmsk","followers_url":"https://api.github.com/users/qwangmsk/followers","following_url":"https://api.github.com/users/qwangmsk/following{/other_user}","gists_url":"https://api.github.com/users/qwangmsk/gists{/gist_id}","starred_url":"https://api.github.com/users/qwangmsk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/qwangmsk/subscriptions","organizations_url":"https://api.github.com/users/qwangmsk/orgs","repos_url":"https://api.github.com/users/qwangmsk/repos","events_url":"https://api.github.com/users/qwangmsk/events{/privacy}","received_events_url":"https://api.github.com/users/qwangmsk/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-07-07T20:54:51Z","updated_at":"2015-07-08T01:00:44Z","closed_at":"2015-07-08T01:00:44Z","body":"Hi RSEM expert:\r\n\r\nWhen running this command: \"rsem-calculate-expression --bam --estimate-rspd   --no-bam-output  --paired-end Aligned.toTranscriptome.out.bam ./rsem-out Quant\", I received an error (see error message below). I wonder what rsem-out.grp is? Could you please give me a hint how to fix it?\r\n\r\nMany thanks,\r\nQingguo\r\n\r\nrsem-parse-alignments ./rsem-out Quant.temp/Quant Quant.stat/Quant b Aligned.toTranscriptome.out.bam -t 3 -tag XM\r\nCannot open ./rsem-out.grp! It may not exist.\r\n\"rsem-parse-alignments ./rsem-out Quant.temp/Quant Quant.stat/Quant b Aligned.toTranscriptome.out.bam -t 3 -tag XM\" failed! Plase check if you provide correct parameters/options for the pipeline!\r\n"}}