{"action":"created","issue":{"url":"https://api.github.com/repos/RobertsLab/resources/issues/484","repository_url":"https://api.github.com/repos/RobertsLab/resources","labels_url":"https://api.github.com/repos/RobertsLab/resources/issues/484/labels{/name}","comments_url":"https://api.github.com/repos/RobertsLab/resources/issues/484/comments","events_url":"https://api.github.com/repos/RobertsLab/resources/issues/484/events","html_url":"https://github.com/RobertsLab/resources/issues/484","id":380495837,"node_id":"MDU6SXNzdWUzODA0OTU4Mzc=","number":484,"title":"blast error on Mox","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":664409261,"node_id":"MDU6TGFiZWw2NjQ0MDkyNjE=","url":"https://api.github.com/repos/RobertsLab/resources/labels/question","name":"question","color":"cc317c","default":true}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-11-14T01:25:08Z","updated_at":"2018-11-14T01:33:35Z","closed_at":"2018-11-14T01:33:36Z","author_association":"CONTRIBUTOR","body":"My slurm output:     \r\n```\r\nBLAST Database error: No alias or index file found for protein database [/gscratch/srlab/graceac9/blastdb/bluecrab/blastdb/bluecrab] in search path [/gscratch/srlab/graceac9/analyses/1113-Cb-blast::]\r\n```\r\n\r\nI made a blastdb with the fasta from [NCBI](https://www.ncbi.nlm.nih.gov/Traces/wgs/?val=GEID01) in [this .ipynb](https://github.com/fish546-2018/grace-Cbairdi-transcriptome/blob/master/notebooks/make_blastn_db.ipynb). \r\n\r\nI uploaded the output files to [owl](http://owl.fish.washington.edu/scaphapoda/grace/Crab-project/bluecrab/), and then used ```rsync``` to get them to Mox.\r\n```\r\n[graceac9@mox2 graceac9]$ cd blastdb/bluecrab/blastdb/\r\n[graceac9@mox2 blastdb]$ ls\r\nbluecrab.fasta\tbluecrab.nhr  bluecrab.nin  bluecrab.nsq\r\n```\r\n\r\nHere is what the ```head``` of the fasta looks like:     \r\n```\r\n[graceac9@mox2 blastdb]$ head bluecrab.fasta \r\n>GEID01000001.1 TSA: Callinectes sapidus C_sapidus_gill_comp0_c0_seq1 transcribed RNA sequence\r\nTGATGCATAGTTGAGGGTGAGGCGCGCCACACCCTCAACTATGCATCGCTGCAGGACAAGCCACTGCCGC\r\nACCAGTGTGTCTTTAAGAAGCACATCGTCAGGATCGAGGGCCAGGGCCTCTTCAGCTTCTCCTGCAACCC\r\nCACCAGCGGCGCGCCGGAGTGGGAGGGAATAGAGTCGATGGAGCAGTATGGGGGCAACACCTGCTCCGTC\r\nAAGGATCAGGTGACAACAGCGTGGGTGGTAATGGTCGTCACCGTCGTGTTGGTGGTGGGGTTCTGTGTTG\r\nTGCTGTACTCCTGTGTGCTGCAGACCCTCCAGGAACGAGCAAGGCGAGAACTGATGGCAACCCACATCCA\r\nATACGGCTACACCTGACCTCTCTGCACACACGCGGCAGGCGAGACGGGCCGGCAGACCTGGAGTGACTAG\r\nACACAGGGATGGTGTGCCCTGTCACCACAACCACCATCACCATCAATGCAAGAACTCAAGGAGGATTGCA\r\nCCCCAAAACACATCACCATCACCACCACCA\r\n>GEID01000002.1 TSA: Callinectes sapidus C_sapidus_gill_comp0_c0_seq2 transcribed RNA sequence\r\n[graceac9@mox2 blastdb]$ pwd\r\n/gscratch/srlab/graceac9/blastdb/bluecrab/blastdb\r\n```\r\n\r\nThe blast .sh script lives on Mox here:    \r\n```/gscratch/srlab/graceac9/jobs/20181113-Cb-bluecrab-blast.sh```"},"comment":{"url":"https://api.github.com/repos/RobertsLab/resources/issues/comments/438504424","html_url":"https://github.com/RobertsLab/resources/issues/484#issuecomment-438504424","issue_url":"https://api.github.com/repos/RobertsLab/resources/issues/484","id":438504424,"node_id":"MDEyOklzc3VlQ29tbWVudDQzODUwNDQyNA==","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},"created_at":"2018-11-14T01:33:35Z","updated_at":"2018-11-14T01:33:35Z","author_association":"CONTRIBUTOR","body":"wow. thanks! in queue"}}
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