{"action":"created","issue":{"url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/263","repository_url":"https://api.github.com/repos/sanger-pathogens/Roary","labels_url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/263/labels{/name}","comments_url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/263/comments","events_url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/263/events","html_url":"https://github.com/sanger-pathogens/Roary/issues/263","id":167055368,"number":263,"title":"Roary 3.6.5 giving different (erroneous) results compared to 3.5.7 and 3.6.1/3.6.3/3.6.4","user":{"login":"dutchscientist","id":10428112,"avatar_url":"https://avatars.githubusercontent.com/u/10428112?v=3","gravatar_id":"","url":"https://api.github.com/users/dutchscientist","html_url":"https://github.com/dutchscientist","followers_url":"https://api.github.com/users/dutchscientist/followers","following_url":"https://api.github.com/users/dutchscientist/following{/other_user}","gists_url":"https://api.github.com/users/dutchscientist/gists{/gist_id}","starred_url":"https://api.github.com/users/dutchscientist/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dutchscientist/subscriptions","organizations_url":"https://api.github.com/users/dutchscientist/orgs","repos_url":"https://api.github.com/users/dutchscientist/repos","events_url":"https://api.github.com/users/dutchscientist/events{/privacy}","received_events_url":"https://api.github.com/users/dutchscientist/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/sanger-pathogens/Roary/labels/bug","name":"bug","color":"fc2929"}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2016-07-22T14:18:23Z","updated_at":"2016-07-26T01:03:41Z","closed_at":"2016-07-25T14:56:06Z","body":"I have just installed a new Biolinux8 workstation and included Roary (of course). It installed v. 3.6.5, and when I used it with a known Campylobacter coli test set, it claimed that there were 0 core, 0 soft core genes, and dumped everything into shell, cloud etc. Even with -i 70 and -s switches.\r\n\r\nI previously used v.3.5.7 and that gave me >1,000 core genes with the same set, and when I downgraded to earlier versions on CPAN (3.6.3 and 3.6.4) and an older one I had on a virtual machine (3.6.1), it also gave me the earlier result of 1,350 core genes. Something has been changed in 3.6.5 that could cause this difference/error?"},"comment":{"url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/comments/235132827","html_url":"https://github.com/sanger-pathogens/Roary/issues/263#issuecomment-235132827","issue_url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/263","id":235132827,"user":{"login":"dutchscientist","id":10428112,"avatar_url":"https://avatars.githubusercontent.com/u/10428112?v=3","gravatar_id":"","url":"https://api.github.com/users/dutchscientist","html_url":"https://github.com/dutchscientist","followers_url":"https://api.github.com/users/dutchscientist/followers","following_url":"https://api.github.com/users/dutchscientist/following{/other_user}","gists_url":"https://api.github.com/users/dutchscientist/gists{/gist_id}","starred_url":"https://api.github.com/users/dutchscientist/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dutchscientist/subscriptions","organizations_url":"https://api.github.com/users/dutchscientist/orgs","repos_url":"https://api.github.com/users/dutchscientist/repos","events_url":"https://api.github.com/users/dutchscientist/events{/privacy}","received_events_url":"https://api.github.com/users/dutchscientist/received_events","type":"User","site_admin":false},"created_at":"2016-07-26T01:03:41Z","updated_at":"2016-07-26T01:03:41Z","body":"This is the output with 3.6.4:\r\n\r\nCore genes\t(99% <= strains <= 100%)\t1350\r\nSoft core genes\t(95% <= strains < 99%)\t20\r\nShell genes\t(15% <= strains < 95%)\t466\r\nCloud genes\t(0% <= strains < 15%)\t1353\r\nTotal genes\t(0% <= strains <= 100%)\t3189\r\n\r\narnoud@T130[roary] roary -v -i 80 -s *.gff                            [ 1:41AM]\r\n\r\nPlease cite Roary if you use any of the results it produces:\r\n    Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill,\r\n\t\"Roary: Rapid large-scale prokaryote pan genome analysis\", Bioinformatics, 2015 Nov 15;31(22):3691-3693\r\n    doi: http://doi.org/10.1093/bioinformatics/btv421\r\n\tPubmed: 26198102\r\n\r\n2016/07/26 01:46:08 Fixing input GFF files\r\n2016/07/26 01:46:25 Extracting proteins from GFF files\r\n<same names>\r\nCombine proteins into a single file\r\nIteratively run cd-hit\r\nParallel all against all blast\r\nCluster with MCL\r\n2016/07/26 01:56:56 Running command: pan_genome_post_analysis -o clustered_proteins -p pan_genome.fa -s gene_presence_absence.csv -c _clustered.clstr  -i /home/arnoud/data/roary/yxviRwP7O8//_gff_files -f /home/arnoud/data/roary/yxviRwP7O8//_fasta_files -t 11  --dont_create_rplots --dont_split_groups  -v  -j Local --processors 1 --group_limit 50000 -cd 99\r\n2016/07/26 01:56:56 Reinflate clusters\r\n2016/07/26 01:56:57 Split groups with paralogs\r\n2016/07/26 01:56:57 Labelling the groups\r\n2016/07/26 01:56:57 Transfering the annotation to the groups\r\n2016/07/26 01:57:15 Creating accessory binary gene presence and absence fasta\r\n2016/07/26 01:57:16 Creating accessory binary gene presence and absence tree\r\n2016/07/26 01:57:16 Running command: /usr/bin/fasttree -fastest -nt accessory_binary_genes.fa > accessory_binary_genes.fa.newick \r\nFastTree Version 2.1.7 SSE3\r\nAlignment: accessory_binary_genes.fa\r\nNucleotide distances: Jukes-Cantor Joins: balanced Support: SH-like 1000\r\nSearch: Fastest+2nd +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1\r\nTopHits: 1.00*sqrtN close=default refresh=0.50\r\nML Model: Jukes-Cantor, CAT approximation with 20 rate categories\r\nInitial topology in 0.02 seconds\r\nRefining topology: 23 rounds ME-NNIs, 2 rounds ME-SPRs, 12 rounds ML-NNIs\r\nTotal branch-length 3.557 after 0.25 sec, 101 of 112 nodes   \r\nML-NNI round 1: LogLk = -13812.193 NNIs 15 max delta 20.13 Time 0.37\r\nSwitched to using 20 rate categories (CAT approximation)1 of 20   \r\nRate categories were divided by 0.853 so that average rate = 1.0\r\nCAT-based log-likelihoods may not be comparable across runs\r\nUse -gamma for approximate but comparable Gamma(20) log-likelihoods\r\nML-NNI round 2: LogLk = -13295.617 NNIs 7 max delta 16.76 Time 0.46\r\nML-NNI round 3: LogLk = -13294.223 NNIs 1 max delta 0.00 Time 0.51\r\nTurning off heuristics for final round of ML NNIs (converged)\r\nML-NNI round 4: LogLk = -13287.413 NNIs 2 max delta 2.06 Time 0.60 (final)\r\nOptimize all lengths: LogLk = -13287.028 Time 0.62\r\nTotal time: 0.81 seconds Unique: 57/62 Bad splits: 0/54"}}
{"actor":{"display_login":"dutchscientist"}}