{"action":"created","issue":{"url":"https://api.github.com/repos/jfass/apc/issues/2","labels_url":"https://api.github.com/repos/jfass/apc/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/jfass/apc/issues/2/comments","events_url":"https://api.github.com/repos/jfass/apc/issues/2/events","html_url":"https://github.com/jfass/apc/issues/2","id":93852007,"number":2,"title":"Irregular last results","user":{"login":"stephenturner","id":460076,"avatar_url":"https://avatars.githubusercontent.com/u/460076?v=3","gravatar_id":"","url":"https://api.github.com/users/stephenturner","html_url":"https://github.com/stephenturner","followers_url":"https://api.github.com/users/stephenturner/followers","following_url":"https://api.github.com/users/stephenturner/following{/other_user}","gists_url":"https://api.github.com/users/stephenturner/gists{/gist_id}","starred_url":"https://api.github.com/users/stephenturner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stephenturner/subscriptions","organizations_url":"https://api.github.com/users/stephenturner/orgs","repos_url":"https://api.github.com/users/stephenturner/repos","events_url":"https://api.github.com/users/stephenturner/events{/privacy}","received_events_url":"https://api.github.com/users/stephenturner/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-07-08T17:59:48Z","updated_at":"2015-07-11T11:07:07Z","closed_at":"2015-07-11T11:07:07Z","body":"Hi Joseph. I ran across this tool and wanted to give it a spin. I have a plasmid assembly and the dot plot tells me it's circular, but the ends are messy.\r\n\r\nI'm trying to run apc on a single 90kb contig and I get the note that I have irregular LAST results. I tried running the commands that appear to be in the perl script, and I look at my alignment file, and this is what I see:\r\n\r\n```\r\n$ lastdb tmp ../hyb-plas120-nanopgm.fasta\r\n\r\n$ lastal -s1 -x300 -f0 -T1 tmp ../hyb-plas120-nanopgm.fasta\r\n# LAST version 548\r\n#\r\n# a=7 b=1 A=7 B=1 c=100000 e=40 d=15 x=300 y=9 z=300\r\n# R=10 u=0 s=1 T=1 m=10 l=1 n=10 k=1 i=8192 w=1000 t=0.910239 g=1 j=3 Q=0\r\n# tmp\r\n# Reference sequences=1 normal letters=94654\r\n#\r\n#    A  C  G  T\r\n# A  1 -1 -1 -1\r\n# C -1  1 -1 -1\r\n# G -1 -1  1 -1\r\n# T -1 -1 -1  1\r\n#\r\n# Coordinates are 0-based.  For - strand matches, coordinates\r\n# in the reverse complement of the 2nd sequence are used.\r\n#\r\n# score\tname1\tstart1\talnSize1\tstrand1\tseqSize1\tname2\tstart2\talnSize2\tstrand2\tseqSize2\tblocks\r\n#\r\n# batch 0\r\n94654\tplasmid_120_nanopore_pgm_corrected_pilon\t0\t94654\t+\t94654\tplasmid_120_nanopore_pgm_corrected_pilon\t0\t94654\t+\t94654\t94654\r\n# Query sequences=1\r\n```\r\n\r\nThat is, a single line, not 3, which is what the script was expecting. Any idea what's going on here? Thanks."},"comment":{"url":"https://api.github.com/repos/jfass/apc/issues/comments/120604138","html_url":"https://github.com/jfass/apc/issues/2#issuecomment-120604138","issue_url":"https://api.github.com/repos/jfass/apc/issues/2","id":120604138,"user":{"login":"stephenturner","id":460076,"avatar_url":"https://avatars.githubusercontent.com/u/460076?v=3","gravatar_id":"","url":"https://api.github.com/users/stephenturner","html_url":"https://github.com/stephenturner","followers_url":"https://api.github.com/users/stephenturner/followers","following_url":"https://api.github.com/users/stephenturner/following{/other_user}","gists_url":"https://api.github.com/users/stephenturner/gists{/gist_id}","starred_url":"https://api.github.com/users/stephenturner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/stephenturner/subscriptions","organizations_url":"https://api.github.com/users/stephenturner/orgs","repos_url":"https://api.github.com/users/stephenturner/repos","events_url":"https://api.github.com/users/stephenturner/events{/privacy}","received_events_url":"https://api.github.com/users/stephenturner/received_events","type":"User","site_admin":false},"created_at":"2015-07-11T11:07:06Z","updated_at":"2015-07-11T11:07:06Z","body":"Thanks for those suggestions. I actually ran into [https://github.com/sanger-pathogens/circlator](circlator) (no \"u\") prior to apc, but with outputs undocumented it's not immediately useful. I took identifyCircularContigs for a spin, but need to dust off my perl to get this working.\r\n\r\nBut you're right, I've got some odd things happening at the end of my assembly. This was a single-contig nanopore-only assembly from celera polished with ion torrent reads using pilon. May warrant another minION run with newer flow cells.\r\n\r\nRE: axis, just used the most recent version of gepard and it was like this out of the box.\r\n\r\nClosing this issue because I believe apc did just what it should have when it reported irregular last results. Only suggestion: echo to screen the command used to run lastdb/lastal. Or add a -verbose option to echo to screen all the commands issued."}}