{"action":"created","issue":{"url":"https://api.github.com/repos/picrust/picrust2/issues/34","repository_url":"https://api.github.com/repos/picrust/picrust2","labels_url":"https://api.github.com/repos/picrust/picrust2/issues/34/labels{/name}","comments_url":"https://api.github.com/repos/picrust/picrust2/issues/34/comments","events_url":"https://api.github.com/repos/picrust/picrust2/issues/34/events","html_url":"https://github.com/picrust/picrust2/issues/34","id":347939608,"node_id":"MDU6SXNzdWUzNDc5Mzk2MDg=","number":34,"title":"EPA-NG not working","user":{"login":"arghya1611","id":34534484,"node_id":"MDQ6VXNlcjM0NTM0NDg0","avatar_url":"https://avatars3.githubusercontent.com/u/34534484?v=4","gravatar_id":"","url":"https://api.github.com/users/arghya1611","html_url":"https://github.com/arghya1611","followers_url":"https://api.github.com/users/arghya1611/followers","following_url":"https://api.github.com/users/arghya1611/following{/other_user}","gists_url":"https://api.github.com/users/arghya1611/gists{/gist_id}","starred_url":"https://api.github.com/users/arghya1611/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arghya1611/subscriptions","organizations_url":"https://api.github.com/users/arghya1611/orgs","repos_url":"https://api.github.com/users/arghya1611/repos","events_url":"https://api.github.com/users/arghya1611/events{/privacy}","received_events_url":"https://api.github.com/users/arghya1611/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-08-06T14:09:01Z","updated_at":"2018-08-07T13:20:02Z","closed_at":null,"author_association":"NONE","body":"Hi\r\nI installed picrust2 on a Ubuntu16.06 VBox a few days back and the EPA-NG step in the sequence placement is not working. The installation was carried out as instructed without a single error. Pytest ran in all greens. I ran place.seqs with print_cmds and this is the error i am getting: \r\n\r\n(picrust2-dev) arghya250@arghya250-VirtualBox:~/Apps/picrust2$ place_seqs.py -s example_files/tutorial.fna -o OUTPUT.tre --threads 10 --intermediate placement_working\r\npapara called as:\r\npapara -t /home/arghya250/Apps/picrust2/default_files/prokaryotic/img_centroid_16S_aligned.tree -s ref_seqs.phylip -q /home/arghya250/Apps/picrust2/example_files/tutorial.fna -j 10 -n out \r\ngap rate: 1503347 21163428\r\ngap rate: 0.0710351\r\nrate matrix: [2,2]((-0.0710351,0.0710351),(0.928965,-0.928965))\r\np: [2,2]((0.99324,0.00675989),(0.0884027,0.911597))\r\nreferences container instantiated as: papara::references<pvec_pgap, sequence_model::tag_dna>\r\nedges: 32885\r\nscoring scheme: -3 -1 2 -3\r\npapara_core version 2.5\r\nstart scoring, using 10 threads\r\nthread 5: 1.22437 gncup/s\r\nthread 6: 1.23993 gncup/s\r\nthread 1: 1.28678 gncup/s\r\nthread 4: 1.26158 gncup/s\r\nthread 3: 1.34938 gncup/s\r\nthread 9: 1.31181 gncup/s\r\nthread 8: 1.28195 gncup/s\r\nthread 0: 1.33646 gncup/s\r\nthread 2: 1.3424 gncup/s\r\nthread 7: 1.26382 gncup/s\r\nscoring finished: 9.65413\r\nsweep: 98658 -> 0\r\n38.1369\r\ngenerating best scoring alignments\r\nSUCCESS 38.1369\r\nINFO Converting given FASTA file to BFAST format...\r\nINFO Resulting bfast file was written to: placement_working/epa_out/study_seqs_papara.fasta.bfast\r\nINFO Selected: Output dir: placement_working/epa_out/\r\nINFO Selected: Query file: placement_working/epa_out/study_seqs_papara.fasta.bfast\r\nINFO Selected: Tree file: /home/arghya250/Apps/picrust2/default_files/prokaryotic/img_centroid_16S_aligned.tree\r\nINFO Selected: Reference MSA: placement_working/ref_seqs_papara.fasta\r\nINFO Selected: Specified model: GTR+G\r\nINFO    Rate heterogeneity: GAMMA (4 cats, mean),  alpha: 1 (ML),  weights&rates: (0.25,0.136954) (0.25,0.476752) (0.25,1) (0.25,2.38629) \r\n        Base frequencies (ML): 0.25 0.25 0.25 0.25 \r\n        Substitution rates (ML): 0.5 0.5 0.5 0.5 0.5 1\r\nINFO Selected: Reading queries in chunks of: 5000\r\nINFO Selected: Using threads: 10\r\nINFO     ______ ____   ___           _   __ ______\r\n        / ____// __ \\ /   |         / | / // ____/\r\n       / __/  / /_/ // /| | ______ /  |/ // / __  \r\n      / /___ / ____// ___ |/_____// /|  // /_/ /  \r\n     /_____//_/    /_/  |_|      /_/ |_/ \\____/ (v0.2.1-beta)\r\nINFO Number of ranks: 1\r\nINFO Output file: placement_working/epa_out/epa_result.jplace\r\nError running this command:\r\nepa-ng --tree /home/arghya250/Apps/picrust2/default_files/prokaryotic/img_centroid_16S_aligned.tree --ref-msa placement_working/ref_seqs_papara.fasta --query placement_working/epa_out/study_seqs_papara.fasta.bfast --chunk-size 5000 -T 10 -m GTR+G -w placement_working/epa_out\r\n\r\nWhats going wrong here ? Please help.\r\n"},"comment":{"url":"https://api.github.com/repos/picrust/picrust2/issues/comments/411052922","html_url":"https://github.com/picrust/picrust2/issues/34#issuecomment-411052922","issue_url":"https://api.github.com/repos/picrust/picrust2/issues/34","id":411052922,"node_id":"MDEyOklzc3VlQ29tbWVudDQxMTA1MjkyMg==","user":{"login":"gavinmdouglas","id":12489683,"node_id":"MDQ6VXNlcjEyNDg5Njgz","avatar_url":"https://avatars0.githubusercontent.com/u/12489683?v=4","gravatar_id":"","url":"https://api.github.com/users/gavinmdouglas","html_url":"https://github.com/gavinmdouglas","followers_url":"https://api.github.com/users/gavinmdouglas/followers","following_url":"https://api.github.com/users/gavinmdouglas/following{/other_user}","gists_url":"https://api.github.com/users/gavinmdouglas/gists{/gist_id}","starred_url":"https://api.github.com/users/gavinmdouglas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/gavinmdouglas/subscriptions","organizations_url":"https://api.github.com/users/gavinmdouglas/orgs","repos_url":"https://api.github.com/users/gavinmdouglas/repos","events_url":"https://api.github.com/users/gavinmdouglas/events{/privacy}","received_events_url":"https://api.github.com/users/gavinmdouglas/received_events","type":"User","site_admin":false},"created_at":"2018-08-07T13:20:02Z","updated_at":"2018-08-07T13:20:02Z","author_association":"CONTRIBUTOR","body":"Hi there,\n\nAre you using the version of EPA-NG that’s packaged in the “placement_tools” folder of the picrust2 rep?\n\n\nBest,\n\nGavin\n\n> On Aug 6, 2018, at 11:09 AM, Arghya Mukherjee <notifications@github.com> wrote:\n> \n> \n> generating best scoring alignments\n> SUCCESS 38.1369\n> INFO Converting given FASTA file to BFAST format...\n> INFO Resulting bfast file was written to: placement_working/epa_out/study_seqs_papara.fasta.bfast\n> INFO Selected: Output dir: placement_working/epa_out/\n> INFO Selected: Query file: placement_working/epa_out/study_seqs_papara.fasta.bfast\n> INFO Selected: Tree file: /home/arghya250/Apps/picrust2/default_files/prokaryotic/img_centroid_16S_aligned.tree\n> INFO Selected: Reference MSA: placement_working/ref_seqs_papara.fasta\n> INFO Selected: Specified model: GTR+G\n> INFO Rate heterogeneity: GAMMA (4 cats, mean), alpha: 1 (ML), weights&rates: (0.25,0.136954) (0.25,0.476752) (0.25,1) (0.25,2.38629)\n> Base frequencies (ML): 0.25 0.25 0.25 0.25\n> Substitution rates (ML): 0.5 0.5 0.5 0.5 0.5 1\n> INFO Selected: Reading queries in chunks of: 5000\n> INFO Selected: Using threads: 10\n> INFO ______ ____ ___ _ __ ______\n> / // __ \\ / | / | / // /\n> / __/ / // // /| | ______ / |/ // / __\n> / / / // ___ |/_____// /| // // /\n> /_____/// // || // |/ __/ (v0.2.1-beta)\n> INFO Number of ranks: 1\n> INFO Output file: placement_working/epa_out/epa_result.jplace\n> Error running this command:\n> epa-ng --tree /home/arghya250/Apps/picrust2/default_files/prokaryotic/img_centroid_16S_aligned.tree --ref-msa placement_working/ref_seqs_papara.fasta --query placement_working/epa_out/study_seqs_papara.fasta.bfast --chunk-size 5000 -T 10 -m GTR+G -w placement_working/epa_out\n> \n> \n\n"}}
{"actor":{"display_login":"gavinmdouglas"}}