{"action":"created","issue":{"url":"https://api.github.com/repos/hsgweon/pipits/issues/17","repository_url":"https://api.github.com/repos/hsgweon/pipits","labels_url":"https://api.github.com/repos/hsgweon/pipits/issues/17/labels{/name}","comments_url":"https://api.github.com/repos/hsgweon/pipits/issues/17/comments","events_url":"https://api.github.com/repos/hsgweon/pipits/issues/17/events","html_url":"https://github.com/hsgweon/pipits/issues/17","id":356556658,"node_id":"MDU6SXNzdWUzNTY1NTY2NTg=","number":17,"title":"pipits_funits","user":{"login":"igo111","id":20595940,"node_id":"MDQ6VXNlcjIwNTk1OTQw","avatar_url":"https://avatars1.githubusercontent.com/u/20595940?v=4","gravatar_id":"","url":"https://api.github.com/users/igo111","html_url":"https://github.com/igo111","followers_url":"https://api.github.com/users/igo111/followers","following_url":"https://api.github.com/users/igo111/following{/other_user}","gists_url":"https://api.github.com/users/igo111/gists{/gist_id}","starred_url":"https://api.github.com/users/igo111/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/igo111/subscriptions","organizations_url":"https://api.github.com/users/igo111/orgs","repos_url":"https://api.github.com/users/igo111/repos","events_url":"https://api.github.com/users/igo111/events{/privacy}","received_events_url":"https://api.github.com/users/igo111/received_events","type":"User","site_admin":false},"labels":[{"id":165429157,"node_id":"MDU6TGFiZWwxNjU0MjkxNTc=","url":"https://api.github.com/repos/hsgweon/pipits/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":8,"created_at":"2018-09-03T16:12:48Z","updated_at":"2018-11-20T03:52:13Z","closed_at":null,"author_association":"NONE","body":"Hi\r\n\r\nI have a problem with running pipits_funits with test dataset \r\n\r\n(pipits_env) bio@biolinux-All-Series:~/pipits$ pipits_funits -i out_seqprep/prepped.fasta -o out_funits -x ITS2 -v\r\npipits_funits 2.2, the PIPITS Project\r\nhttps://github.com/hsgweon/pipits\r\n---------------------------------\r\n\r\n2018-09-03 18:59:17 pipits_funits started\r\n2018-09-03 18:59:17 Checking input FASTA for illegal characters\r\n2018-09-03 18:59:17 ... done\r\n2018-09-03 18:59:17 Counting input sequences\r\n2018-09-03 18:59:17 ... number of input sequences: 53\r\n2018-09-03 18:59:17 Dereplicating sequences for efficiency\r\nvsearch v2.8.2_linux_x86_64, 15.6GB RAM, 8 cores\r\nhttps://github.com/torognes/vsearch\r\n\r\nDereplicating file out_seqprep/prepped.fasta 100%\r\n13859 nt in 53 seqs, min 239, max 370, avg 261\r\nSorting 100%\r\n20 unique sequences, avg cluster 2.6, median 2, max 11\r\nWriting output file 100%\r\nWriting uc file, first partSegmentation fault (core dumped)\r\n2018-09-03 18:59:17 Error: None zero returncode: vsearch --derep_fulllength out_seqprep/prepped.fasta --output out_funits/intermediate/derep.fasta --uc out_funits/intermediate/derep.uc --fasta_width 0 —sizeout\r\n\r\nDo you have solution for this?\r\nThank you for your help."},"comment":{"url":"https://api.github.com/repos/hsgweon/pipits/issues/comments/440128769","html_url":"https://github.com/hsgweon/pipits/issues/17#issuecomment-440128769","issue_url":"https://api.github.com/repos/hsgweon/pipits/issues/17","id":440128769,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0MDEyODc2OQ==","user":{"login":"AMFBio","id":44623561,"node_id":"MDQ6VXNlcjQ0NjIzNTYx","avatar_url":"https://avatars1.githubusercontent.com/u/44623561?v=4","gravatar_id":"","url":"https://api.github.com/users/AMFBio","html_url":"https://github.com/AMFBio","followers_url":"https://api.github.com/users/AMFBio/followers","following_url":"https://api.github.com/users/AMFBio/following{/other_user}","gists_url":"https://api.github.com/users/AMFBio/gists{/gist_id}","starred_url":"https://api.github.com/users/AMFBio/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AMFBio/subscriptions","organizations_url":"https://api.github.com/users/AMFBio/orgs","repos_url":"https://api.github.com/users/AMFBio/repos","events_url":"https://api.github.com/users/AMFBio/events{/privacy}","received_events_url":"https://api.github.com/users/AMFBio/received_events","type":"User","site_admin":false},"created_at":"2018-11-20T03:52:13Z","updated_at":"2018-11-20T03:52:13Z","author_association":"NONE","body":"Hi @hsgweon \r\n\r\nI'm getting a similar error as above: [[0m Error: None zero returncode: vsearch --uchime_ref out_process/intermediate/input_nr_otus.fasta --db $PIPITS_UNITE_REFERENCE_DATA_CHIMERA --nonchimeras out_process/intermediate/inp$\r\n\r\nI downgraded to vsearch 2.8.0 however I'm still getting this exact error.\r\n\r\nAre you able to shed any light on this?\r\n\r\nCheers\r\n\r\n\r\n"}}
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