{"action":"created","issue":{"url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/555","repository_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq","labels_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/555/labels{/name}","comments_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/555/comments","events_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/555/events","html_url":"https://github.com/trinityrnaseq/trinityrnaseq/issues/555","id":352679053,"node_id":"MDU6SXNzdWUzNTI2NzkwNTM=","number":555,"title":"Error during Transcript expression quantitation using RSEM","user":{"login":"vivekabarath","id":39739921,"node_id":"MDQ6VXNlcjM5NzM5OTIx","avatar_url":"https://avatars2.githubusercontent.com/u/39739921?v=4","gravatar_id":"","url":"https://api.github.com/users/vivekabarath","html_url":"https://github.com/vivekabarath","followers_url":"https://api.github.com/users/vivekabarath/followers","following_url":"https://api.github.com/users/vivekabarath/following{/other_user}","gists_url":"https://api.github.com/users/vivekabarath/gists{/gist_id}","starred_url":"https://api.github.com/users/vivekabarath/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/vivekabarath/subscriptions","organizations_url":"https://api.github.com/users/vivekabarath/orgs","repos_url":"https://api.github.com/users/vivekabarath/repos","events_url":"https://api.github.com/users/vivekabarath/events{/privacy}","received_events_url":"https://api.github.com/users/vivekabarath/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-08-21T19:32:36Z","updated_at":"2018-08-27T15:53:18Z","closed_at":null,"author_association":"NONE","body":"Hi Brian,\r\n\r\nA Good day to you.\r\n\r\nI am trying to do transcript expression quantitation for a transcriptome generated from paired-end RNA-seq data from 24 files. I have run into an error which I can't understand \r\n\r\nI ran the align_and_estimate_abundance.pl using the following parameters:\r\n\r\nalign_and_estimate_abundance.pl --seqType fq \\\r\n        --samples_file /scratch/Trinity_Run_3/Sample_File_1.txt \\\r\n         --transcripts trinity_out_dir/Trinity.fasta  \\\r\n         --est_method RSEM  --aln_method bowtie2 \\\r\n         --trinity_mode --prep_reference \\\r\n         --output_dir RSEM \\\r\n\t > Transcript_expression_quantitation_using_RSEM.log 2>&1 & \r\n\r\nThe output saved in Transcript_expression_quantitation_using_RSEM.log is as attached. The Sample_File_1.txt is also attached. \r\n[Transcript_expression_quantitation_using_RSEM.log](https://github.com/trinityrnaseq/trinityrnaseq/files/2307749/Transcript_expression_quantitation_using_RSEM.log)\r\n[Sample_File_1.txt](https://github.com/trinityrnaseq/trinityrnaseq/files/2307748/Sample_File_1.txt)\r\n\r\n\r\nKindly Help.\r\n\r\nWith best regards\r\n\r\nBaradwaj\r\n"},"comment":{"url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/comments/416273701","html_url":"https://github.com/trinityrnaseq/trinityrnaseq/issues/555#issuecomment-416273701","issue_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/555","id":416273701,"node_id":"MDEyOklzc3VlQ29tbWVudDQxNjI3MzcwMQ==","user":{"login":"brianjohnhaas","id":7542111,"node_id":"MDQ6VXNlcjc1NDIxMTE=","avatar_url":"https://avatars0.githubusercontent.com/u/7542111?v=4","gravatar_id":"","url":"https://api.github.com/users/brianjohnhaas","html_url":"https://github.com/brianjohnhaas","followers_url":"https://api.github.com/users/brianjohnhaas/followers","following_url":"https://api.github.com/users/brianjohnhaas/following{/other_user}","gists_url":"https://api.github.com/users/brianjohnhaas/gists{/gist_id}","starred_url":"https://api.github.com/users/brianjohnhaas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brianjohnhaas/subscriptions","organizations_url":"https://api.github.com/users/brianjohnhaas/orgs","repos_url":"https://api.github.com/users/brianjohnhaas/repos","events_url":"https://api.github.com/users/brianjohnhaas/events{/privacy}","received_events_url":"https://api.github.com/users/brianjohnhaas/received_events","type":"User","site_admin":false},"created_at":"2018-08-27T15:53:18Z","updated_at":"2018-08-27T15:53:18Z","author_association":"MEMBER","body":"hi - can you try using the kallisto or salmon options for quantification and see how that goes?  Debugging rsem issues isn't much fun."}}
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