{"action":"created","issue":{"url":"https://api.github.com/repos/marbl/metAMOS/issues/223","labels_url":"https://api.github.com/repos/marbl/metAMOS/issues/223/labels{/name}","comments_url":"https://api.github.com/repos/marbl/metAMOS/issues/223/comments","events_url":"https://api.github.com/repos/marbl/metAMOS/issues/223/events","html_url":"https://github.com/marbl/metAMOS/issues/223","id":93878040,"number":223,"title":"Error during validate, iMetamos","user":{"login":"ptmckenney","id":6034375,"avatar_url":"https://avatars.githubusercontent.com/u/6034375?v=3","gravatar_id":"","url":"https://api.github.com/users/ptmckenney","html_url":"https://github.com/ptmckenney","followers_url":"https://api.github.com/users/ptmckenney/followers","following_url":"https://api.github.com/users/ptmckenney/following{/other_user}","gists_url":"https://api.github.com/users/ptmckenney/gists{/gist_id}","starred_url":"https://api.github.com/users/ptmckenney/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ptmckenney/subscriptions","organizations_url":"https://api.github.com/users/ptmckenney/orgs","repos_url":"https://api.github.com/users/ptmckenney/repos","events_url":"https://api.github.com/users/ptmckenney/events{/privacy}","received_events_url":"https://api.github.com/users/ptmckenney/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-07-08T20:05:30Z","updated_at":"2015-07-24T11:53:52Z","closed_at":null,"body":"Hi I'm getting an error during the validate phase running iMetamos:\r\n\r\n```\r\ninitpipeline -W imetamos -1 UT-1_GTCCGC_L001_R1_001.fastq -2 UT-1_GTCCGC_L001_R2_001.fastq -d /Applications/metAMOS-1.5rc3/Peter/UT_test_metamos -i 100:300\r\n\r\nrunpipeline -d /Applications/metAMOS-1.5rc3/Peter/UT_test_metamos\r\n```\r\n\r\nThe error message at terminal:\r\n```\r\nStarting Task = validate.VALIDATE\r\n*** metAMOS: Error, type SNP is not available, skipping\r\nWarning: selected score LAP was not available, skipping it\r\nWarning: selected score ALE was not available, skipping it\r\nWarning: selected score CGAL was not available, skipping it\r\nWarning: selected score SNP was not available, skipping it\r\nWarning: selected score FRCBAM was not available, skipping it\r\nWarning: selected score ORF was not available, skipping it\r\nWarning: selected score REAPR was not available, skipping it\r\nWarning: selected score N50 was not available, skipping it\r\nrecruiting genomes..\r\nError: recruiting references failed\r\nWarning: could not recruit any references\r\n \r\nOops, MetAMOS finished with errors! see text in red above for details.\r\n```\r\n\r\nThis was in the VALIDATE.log:\r\n```\r\nunlink: /Applications/metAMOS-1.5rc3/Peter/UT_test_metamos/Assemble/out/proba.asm.contig: No such file or directory\r\nunlink: /Applications/metAMOS-1.5rc3/Peter/UT_test_metamos/Assemble/out/proba.asm.contig: No such file or directory\r\nln: /Applications/metAMOS-1.5rc3/Peter/UT_test_metamos/Assemble/out/.asm.contig: No such file or directory\r\nunlink: /Applications/metAMOS-1.5rc3/Peter/UT_test_metamos/Assemble/out/proba.linearize.scaffolds.final: No such file or directory\r\nln: /Applications/metAMOS-1.5rc3/Peter/UT_test_metamos/Assemble/out/.asm.contig: No such file or directory\r\nunlink: /Applications/metAMOS-1.5rc3/Peter/UT_test_metamos/Assemble/out/proba.asm.tigr: No such file or directory\r\nln: /Applications/metAMOS-1.5rc3/Peter/UT_test_metamos/Assemble/out/.asm.tigr: No such file or directory\r\nunlink: /Applications/metAMOS-1.5rc3/Peter/UT_test_metamos/Assemble/out/proba.contig.cnt: No such file or directory\r\nln: /Applications/metAMOS-1.5rc3/Peter/UT_test_metamos/Assemble/out/.contig.cnt: No such file or directory\r\nunlink: /Applications/metAMOS-1.5rc3/Peter/UT_test_metamos/Assemble/out/proba.contig.cvg: No such file or directory\r\nln: /Applications/metAMOS-1.5rc3/Peter/UT_test_metamos/Assemble/out/.contig.cvg: No such file or directory\r\nunlink: /Applications/metAMOS-1.5rc3/Peter/UT_test_metamos/Assemble/out/proba.afg: No such file or directory\r\n```\r\n\r\nThanks!\r\nPeter."},"comment":{"url":"https://api.github.com/repos/marbl/metAMOS/issues/comments/124498382","html_url":"https://github.com/marbl/metAMOS/issues/223#issuecomment-124498382","issue_url":"https://api.github.com/repos/marbl/metAMOS/issues/223","id":124498382,"user":{"login":"ptmckenney","id":6034375,"avatar_url":"https://avatars.githubusercontent.com/u/6034375?v=3","gravatar_id":"","url":"https://api.github.com/users/ptmckenney","html_url":"https://github.com/ptmckenney","followers_url":"https://api.github.com/users/ptmckenney/followers","following_url":"https://api.github.com/users/ptmckenney/following{/other_user}","gists_url":"https://api.github.com/users/ptmckenney/gists{/gist_id}","starred_url":"https://api.github.com/users/ptmckenney/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ptmckenney/subscriptions","organizations_url":"https://api.github.com/users/ptmckenney/orgs","repos_url":"https://api.github.com/users/ptmckenney/repos","events_url":"https://api.github.com/users/ptmckenney/events{/privacy}","received_events_url":"https://api.github.com/users/ptmckenney/received_events","type":"User","site_admin":false},"created_at":"2015-07-24T11:53:52Z","updated_at":"2015-07-24T11:53:52Z","body":"Hi\r\n\r\nI performed the installation as listed in the docs using INSTALL.py. First the core, then iMetamos then optional.\r\n\r\nWhen I run Metamos I get these warnings:\r\n\r\n```\r\nWarning: Celera Assembler is not found, some functionality will not be available\r\nWarning: BLASR is not found, some functionality will not be available\r\nWarning: Newbler is not found, some functionality will not be available\r\nWarning: SparseAssembler is not found, some functionality will not be available\r\nWarning: MetaGeneMark is not found, some functionality will not be available\r\nWarning: SignalP+ is not found, some functionality will not be available\r\nWarning: PHmmer is not found, some functionality will not be available\r\nWarning: FreeBayes is not found, some functionality will not be available\r\n```"}}