{"action":"opened","issue":{"url":"https://api.github.com/repos/RobertsLab/resources/issues/452","repository_url":"https://api.github.com/repos/RobertsLab/resources","labels_url":"https://api.github.com/repos/RobertsLab/resources/issues/452/labels{/name}","comments_url":"https://api.github.com/repos/RobertsLab/resources/issues/452/comments","events_url":"https://api.github.com/repos/RobertsLab/resources/issues/452/events","html_url":"https://github.com/RobertsLab/resources/issues/452","id":373702404,"node_id":"MDU6SXNzdWUzNzM3MDI0MDQ=","number":452,"title":"Trinity: Error; cannot find path to bowtie2 ","user":{"login":"grace-ac","id":14934314,"node_id":"MDQ6VXNlcjE0OTM0MzE0","avatar_url":"https://avatars0.githubusercontent.com/u/14934314?v=4","gravatar_id":"","url":"https://api.github.com/users/grace-ac","html_url":"https://github.com/grace-ac","followers_url":"https://api.github.com/users/grace-ac/followers","following_url":"https://api.github.com/users/grace-ac/following{/other_user}","gists_url":"https://api.github.com/users/grace-ac/gists{/gist_id}","starred_url":"https://api.github.com/users/grace-ac/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/grace-ac/subscriptions","organizations_url":"https://api.github.com/users/grace-ac/orgs","repos_url":"https://api.github.com/users/grace-ac/repos","events_url":"https://api.github.com/users/grace-ac/events{/privacy}","received_events_url":"https://api.github.com/users/grace-ac/received_events","type":"User","site_admin":false},"labels":[{"id":665341898,"node_id":"MDU6TGFiZWw2NjUzNDE4OTg=","url":"https://api.github.com/repos/RobertsLab/resources/labels/Mox%20(hyak)","name":"Mox (hyak)","color":"0052cc","default":false},{"id":664409261,"node_id":"MDU6TGFiZWw2NjQ0MDkyNjE=","url":"https://api.github.com/repos/RobertsLab/resources/labels/question","name":"question","color":"cc317c","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-10-24T22:29:00Z","updated_at":"2018-10-24T22:29:00Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"Here's what I have, basing off of what @kubu4  has done in [his notebook](http://onsnetwork.org/kubu4/2018/09/19/transcriptome-assembly-olympia-oyster-rnaseq-data-with-trinity/)    \r\n\r\n**Questions**\r\n1. Does everything look ok?\r\n2. What do I do about bowtie2 error? \r\n\r\n```\r\n[graceac9@mox1 srlab]$ pwd\r\n/gscratch/srlab\r\n[graceac9@mox1 srlab]$ #!/bin/bash\r\n[graceac9@mox1 srlab]$ ## Job Name\r\n[graceac9@mox1 srlab]$ #SBATCH --job-name=20181024_Cbairdi_trinity_01\r\n[graceac9@mox1 srlab]$ ## Allocation Definition \r\n[graceac9@mox1 srlab]$ #SBATCH --account=srlab\r\n[graceac9@mox1 srlab]$ #SBATCH --partition=srlab\r\n[graceac9@mox1 srlab]$ ## Resources\r\n[graceac9@mox1 srlab]$ ## Nodes \r\n[graceac9@mox1 srlab]$ #SBATCH --nodes=1   \r\n[graceac9@mox1 srlab]$ ## Walltime (days-hours:minutes:seconds format)\r\n[graceac9@mox1 srlab]$ #SBATCH --time=90:30:00\r\n[graceac9@mox1 srlab]$ ## Memory per node\r\n[graceac9@mox1 srlab]$ #SBATCH --mem=500G\r\n[graceac9@mox1 srlab]$ ## Specify the working directory for this job\r\n[graceac9@mox1 srlab]$ #SBATCH --workdir=/gscratch/srlab/graceac9/analyses/1024\r\n[graceac9@mox1 srlab]$ \r\n[graceac9@mox1 srlab]$ /gscratch/srlab/programs/trinity/Trinity \\\r\n> --seqType fq \\\r\n> --max_memory 100G \\\r\n> --left /gscratch/srlab/graceac9/data/304428_S1_L001_R1_001.fastq,\\\r\n> /gscratch/srlab/graceac9/data/304428_S1_L002_R1_001.fastq \\\r\n> --right /gscratch/srlab/graceac9/data/304428_S1_L001_R2_001.fastq,\\\r\n> /gscratch/srlab/graceac9/data/304428_S1_L002_R2_001.fastq \\\r\n> --trimmomatic \\\r\n> --CPU 28\r\nLeft read files: $VAR1 = [\r\n          '/gscratch/srlab/graceac9/data/304428_S1_L001_R1_001.fastq',\r\n          '/gscratch/srlab/graceac9/data/304428_S1_L002_R1_001.fastq'\r\n        ];\r\nRight read files: $VAR1 = [\r\n          '/gscratch/srlab/graceac9/data/304428_S1_L001_R2_001.fastq',\r\n          '/gscratch/srlab/graceac9/data/304428_S1_L002_R2_001.fastq'\r\n        ];\r\nTrinity version: Trinity-v2.4.0\r\n** NOTE: Latest version of Trinity is Trinity-v2.8.4, and can be obtained at:\r\n\thttps://github.com/trinityrnaseq/trinityrnaseq/releases\r\n\r\nwhich: no bowtie2 in (/gscratch/srlab/programs/trinity/trinity-plugins/BIN:/sw/local/bin:/usr/lib64/qt-3.3/bin:/sw/modules-1.775/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lusers/graceac9/bin)\r\nwhich: no bowtie2-build in (/gscratch/srlab/programs/trinity/trinity-plugins/BIN:/sw/local/bin:/usr/lib64/qt-3.3/bin:/sw/modules-1.775/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lusers/graceac9/bin)\r\nError, cannot find path to bowtie2 () or bowtie2-build (), which is now needed as part of Chrysalis' read scaffolding step.  If you should choose to not run bowtie, include the --no_bowtie in your Trinity command."}}
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