{"action":"created","issue":{"url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/221","labels_url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/221/labels{/name}","comments_url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/221/comments","events_url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/221/events","html_url":"https://github.com/sanger-pathogens/Roary/issues/221","id":125249165,"number":221,"title":"roary_plots.py generating flawed plots","user":{"login":"swlong","id":2158927,"avatar_url":"https://avatars.githubusercontent.com/u/2158927?v=3","gravatar_id":"","url":"https://api.github.com/users/swlong","html_url":"https://github.com/swlong","followers_url":"https://api.github.com/users/swlong/followers","following_url":"https://api.github.com/users/swlong/following{/other_user}","gists_url":"https://api.github.com/users/swlong/gists{/gist_id}","starred_url":"https://api.github.com/users/swlong/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/swlong/subscriptions","organizations_url":"https://api.github.com/users/swlong/orgs","repos_url":"https://api.github.com/users/swlong/repos","events_url":"https://api.github.com/users/swlong/events{/privacy}","received_events_url":"https://api.github.com/users/swlong/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2016-01-06T19:50:38Z","updated_at":"2016-01-12T11:18:18Z","closed_at":null,"body":"I am running roary_plots.py after successfully running Roary as well as FastTree similar to the instructions provided, and the following occurs:\r\n\r\n1) A warning is generated: \r\nFutureWarning: order is deprecated. use sort_values(...)\r\nidx = roary.sum(axis=1).order(ascending=False).index\r\n\r\n2) The three plots are generated but they are all erroneous in one way or another.\r\n- The pangenome_matrix.png appears to have a valid matrix but the tree is non-existant, just a straight line. If I open the newick file in dendroscope, it appears valid (ie. it exists).\r\n- The pangenome_pie.png is essentially empty - a straight line w/ zeros and labels superimposed is all that is present\r\n- The pangenome_frequency.png lists tens of thousands of genomes on the X axis (instead of the 51 that were used) and the distribution as presented appears to be incorrect, or doesn't represent the distribution of genes between the 51 genomes present in the pangenome. \r\n\r\n3) Unsure if it is related, but I am finding the following error generated apparently during the MAFFT step (apologies if this is a completely separate issue, I'll branch to a different issue report): \r\n------------- EXCEPTION: Bio::Root::Exception -------------\r\nMSG: Could not open pan_genome_sequences/group_16429.fa.aln: No such file or directory\r\nSTACK: Error::throw\r\nSTACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:486\r\nSTACK: Bio::Root::IO::_initialize_io /usr/share/perl5/Bio/Root/IO.pm:351\r\nSTACK: Bio::SeqIO::_initialize /usr/share/perl5/Bio/SeqIO.pm:491\r\nSTACK: Bio::SeqIO::fasta::_initialize /usr/share/perl5/Bio/SeqIO/fasta.pm:87\r\nSTACK: Bio::SeqIO::new /usr/share/perl5/Bio/SeqIO.pm:372\r\nSTACK: Bio::SeqIO::new /usr/share/perl5/Bio/SeqIO.pm:413\r\nSTACK: Bio::Roary::SortFasta::_input_seqio /usr/local/share/perl/5.18.2/Bio/Roary/SortFasta.pm:27\r\nSTACK: Bio::Roary::SortFasta::sort_fasta /usr/local/share/perl/5.18.2/Bio/Roary/SortFasta.pm:68\r\nSTACK: Bio::Roary::CommandLine::GeneAlignmentFromNucleotides::run /usr/local/share/perl/5.18.2/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm:107\r\nSTACK: /usr/local/bin/protein_alignment_from_nucleotides:14\r\n-----------------------------------------------------------\r\n\r\nThis seems to be happening for some (but not all) clusters... yet core_gene_alignment.aln is still being generated and contains data. \r\n\r\nHas anyone else seen this problem? I will attach example data momentarily. I am running Roary on a Biolinux 8 box.\r\n\r\nBest,\r\nS. W. Long\r\n"},"comment":{"url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/comments/170879957","html_url":"https://github.com/sanger-pathogens/Roary/issues/221#issuecomment-170879957","issue_url":"https://api.github.com/repos/sanger-pathogens/Roary/issues/221","id":170879957,"user":{"login":"andrewjpage","id":24151,"avatar_url":"https://avatars.githubusercontent.com/u/24151?v=3","gravatar_id":"","url":"https://api.github.com/users/andrewjpage","html_url":"https://github.com/andrewjpage","followers_url":"https://api.github.com/users/andrewjpage/followers","following_url":"https://api.github.com/users/andrewjpage/following{/other_user}","gists_url":"https://api.github.com/users/andrewjpage/gists{/gist_id}","starred_url":"https://api.github.com/users/andrewjpage/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/andrewjpage/subscriptions","organizations_url":"https://api.github.com/users/andrewjpage/orgs","repos_url":"https://api.github.com/users/andrewjpage/repos","events_url":"https://api.github.com/users/andrewjpage/events{/privacy}","received_events_url":"https://api.github.com/users/andrewjpage/received_events","type":"User","site_admin":false},"created_at":"2016-01-12T11:18:18Z","updated_at":"2016-01-12T11:18:18Z","body":"Thanks for the data. It looks like Roary ran to completion. I reran the roary_plots script and it produced a proper tree, so I suspect theres an issue with versioning of the python dependancies for this script (Phylo).  We'll take a look to see if we can track it down.\r\n\r\nJSCandy should be able to show you the same information (its an experimental interactive viewer) if you want to give it a shot. Once you load up your data you can change the viewing mode by clicking on the JSCandy logo. \r\nhttp://jameshadfield.github.io/JScandy/\r\n\r\nTheres also the roary2svg.pl script which gives a similar view (but not against a tree).\r\n"}}