{"action":"closed","issue":{"url":"https://api.github.com/repos/marbl/metAMOS/issues/194","labels_url":"https://api.github.com/repos/marbl/metAMOS/issues/194/labels{/name}","comments_url":"https://api.github.com/repos/marbl/metAMOS/issues/194/comments","events_url":"https://api.github.com/repos/marbl/metAMOS/issues/194/events","html_url":"https://github.com/marbl/metAMOS/issues/194","id":67701078,"number":194,"title":"error with run_pipeline_test.sh ","user":{"login":"Ramanandan","id":11878969,"avatar_url":"https://avatars.githubusercontent.com/u/11878969?v=3","gravatar_id":"","url":"https://api.github.com/users/Ramanandan","html_url":"https://github.com/Ramanandan","followers_url":"https://api.github.com/users/Ramanandan/followers","following_url":"https://api.github.com/users/Ramanandan/following{/other_user}","gists_url":"https://api.github.com/users/Ramanandan/gists{/gist_id}","starred_url":"https://api.github.com/users/Ramanandan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Ramanandan/subscriptions","organizations_url":"https://api.github.com/users/Ramanandan/orgs","repos_url":"https://api.github.com/users/Ramanandan/repos","events_url":"https://api.github.com/users/Ramanandan/events{/privacy}","received_events_url":"https://api.github.com/users/Ramanandan/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-04-10T23:12:02Z","updated_at":"2015-04-14T18:44:54Z","closed_at":"2015-04-14T18:44:54Z","body":"Dear Treangen/metAMOS support team,\r\n\r\nAfter running the commnad \"$ python INSTALL.py iMetAMOS\".  I followed the instructions in \"2.2.4\r\nRunning the test suit\" \r\n$ cd ./Test\r\n$ ./run_pipeline_test.sh\r\n\r\nI encountered the following error. In my local machine, I have 24GB RAM. \r\n\r\nprabhakaranra@prabhakaranra-P8X58-AS:~/metAMOS-1.5rc3/Test$ ./run_pipeline_test.sh \r\nError: cannot find BLAST DB directory, expected it in /home/prabhakaranra/metAMOS-1.5rc3/Utilities/DB/. Disabling blastdb dependent programs\r\nProject directory already exists, please specify another\r\nAlternatively, use runPipeline to run an existing project\r\nError: cannot find BLAST DB directory, expected it in /home/prabhakaranra/metAMOS-1.5rc3/Utilities/DB/. Disabling blastdb dependent programs\r\nError: cannot find BLAST DB directory, expected it in /home/prabhakaranra/metAMOS-1.5rc3/Utilities/DB/. Disabling blastdb dependent programs\r\n**no blast DB directory available, disabling steps requiring BLAST DB\r\n[Steps to be skipped]:  set(['FunctionalAnnotation', 'FindRepeats'])\r\nStarting Task = runpipeline.RUNPIPELINE\r\nStarting metAMOS pipeline\r\nError: cannot find BLAST DB directory, expected it in /home/prabhakaranra/metAMOS-1.5rc3/Utilities/DB/. Disabling blastdb dependent programs\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: MetaGeneMark is not found, some functionality will not be available\r\nWarning: SignalP+ is not found, some functionality will not be available\r\nWarning: metaphylerClassify is not found, some functionality will not be available\r\nWarning: PHmmer is not found, some functionality will not be available\r\nWarning: PhyloSift was not found, will not be available\r\n\r\nWarning: FRCbam is not found, some functionality will not be available\r\nWarning: MPI is not available, some functionality may not be available\r\n[Available RAM: 19 GB]\r\n\u001B[\tThere is *19 GB of RAM currently available on this machine, suggested minimum of 32 GB\r\n\u001B[\t*Enabling low MEM mode, might slow down some steps in pipeline\r\n\u001B[\t*If more RAM is available than what is listed above, please close down other programs and restart runPipeline\r\n\r\n________________________________________\r\nTasks which will be run:\r\n\r\nTask = assemble.SplitAssemblers\r\nTask = assemble.Assemble\r\nTask = assemble.CheckAsmResults\r\nTask = assemble.SplitMappers\r\nTask = mapreads.MapReads\r\nTask = mapreads.CheckMapResults\r\nTask = mapreads.SplitForORFs\r\nTask = findorfs.FindORFS\r\nTask = validate.Validate\r\nTask = findreps.FindRepeats\r\nTask = annotate.Annotate\r\nTask = fannotate.FunctionalAnnotation\r\nTask = scaffold.Scaffold\r\nTask = findscforfs.FindScaffoldORFS\r\nTask = abundance.Abundance\r\nTask = propagate.Propagate\r\nTask = classify.Classify\r\nTask = postprocess.Postprocess\r\n________________________________________\r\nWarning: Graphviz is not found, some functionality will not be available\r\nmetAMOS configuration summary:\r\nmetAMOS Version:\tv1.5rc2 \"Praline Brownie\"  workflows: core,imetamos\r\nTime and Date:\t\t2015-04-10\r\nWorking directory:\t/home/prabhakaranra/metAMOS-1.5rc3/Test/test1\r\nPrefix:\t\t\tproba\r\nK-Mer:\t\t\t55\r\nThreads:\t\t15\r\nTaxonomic level:\tclass\r\nVerbose:\t\tFalse\r\nSteps to skip:\t\tMultiAlign, FunctionalAnnotation, FindRepeats\r\nSteps to force:\t\tAbundance, FindORFS, Annotate, Propagate, MapReads, Assemble, FindScaffoldORFS, Classify\r\n\r\n[citation]\r\nMetAMOS\r\n\tTreangen, TJ ⇔  Koren, S, Sommer, DD, Liu, B, Astrovskaya, I, Ondov, B, Darling AE, Phillippy AM, Pop, M. MetAMOS: a modular and open source metagenomic assembly and analysis pipeline. Genome biology, 14(1), R2, 2013.\r\n\r\n\r\nStep-specific configuration:\r\n[abundance]\r\nMetaPhyler\r\n\t\r\n\tLiu B, Gibbons T, Ghodsi M, Treangen T, Pop M. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. BMC Genomics. 2011;12 Suppl 2:S4. Epub 2011 Jul 27.\r\n\r\n[multialign]\r\nM-GCAT\r\n\t/home/prabhakaranra/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64\r\n\tTreangen TJ, Messeguer X. M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. BMC Bioinformatics, 2006.\r\n\r\n[fannotate]\r\nBLAST\r\n\t/home/prabhakaranra/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64\r\n\tAltschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403-10.\r\n\r\n[scaffold]\r\nBambus 2\r\n\t/home/prabhakaranra/metAMOS-1.5rc3/AMOS/Linux-x86_64/bin\r\n\tKoren S, Treangen TJ, Pop M. Bambus 2: scaffolding metagenomes. Bioinformatics 27(21): 2964-2971 2011.\r\n\r\n[findorfs]\r\nFragGeneScan\r\n\t/home/prabhakaranra/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64\r\n\tRho M, Tang H, Ye Y: FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Research 2010, 38:e191-e191.\r\n\r\n[annotate]\r\nKraken\r\n\t/home/prabhakaranra/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/kraken/bin\r\n\tWood DE, Salzberg SL: Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology 2014, 15:R46.\r\n\r\n[assemble]\r\nSOAPdenovo\r\n\t/home/prabhakaranra/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64\r\n\tLi Y, Hu Y, Bolund L, Wang J: State of the art de novo assembly of human genomes from massively parallel sequencing data.Human genomics 2010, 4:271-277.\r\n\r\n[mapreads]\r\nBowtie\r\n\t/home/prabhakaranra/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64\r\n\tLangmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):R25. Epub 2009 Mar 4.\r\n\r\n[preprocess]\r\nmetAMOS built-in filtering\r\n\tN/A\r\n\r\n[validate]\r\nLAP\r\n\t/home/prabhakaranra/metAMOS-1.5rc3/LAP\r\n\tGhodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M. De novo likelihood-based measures for comparing genome assemblies. BMC research notes 6:334, 2013.\r\n\r\n[other]\r\nKrona\r\n\t/home/prabhakaranra/metAMOS-1.5rc3/KronaTools/bin\r\n\tOndov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC Bioinformatics. 2011 Sep 30;12:385.\r\n\r\n\r\nsh: 1: Syntax error: Bad fd number\r\nStarting Task = assemble.ASSEMBLE\r\n    Job  = [preprocess.success -> *.run] completed\r\nCompleted Task = assemble.SplitAssemblers\r\n    Job  = [soapdenovo.55.run -> soapdenovo.55.asm.contig] completed\r\nCompleted Task = assemble.Assemble\r\n    Job  = [[soapdenovo.55.asm.contig] -> [assemble.ok]] completed\r\nCompleted Task = assemble.CheckAsmResults\r\nUptodate Task = assemble.SplitMappers\r\n \r\nStarting Task = mapreads.MAPREADS\r\n    Job  = [soapdenovo.55.asm.contig -> soapdenovo.55.contig.cvg] completed\r\nCompleted Task = mapreads.MapReads\r\n    Job  = [[soapdenovo.55.contig.cvg] -> [mapreads.ok]] completed\r\nCompleted Task = mapreads.CheckMapResults\r\nUptodate Task = mapreads.SplitForORFs\r\nStarting Task = findorfs.FINDORFS\r\n    Job  = [soapdenovo.55.contig.cvg -> soapdenovo.55.faa] completed\r\nCompleted Task = findorfs.FindORFS\r\nStarting Task = validate.VALIDATE\r\n    Job  = [[soapdenovo.55.faa] -> [validate.ok]] completed\r\nCompleted Task = validate.Validate\r\nStarting Task = findrepeats.FINDREPEATS\r\n    Job  = [proba.fna -> proba.repeats] completed\r\nCompleted Task = findreps.FindRepeats\r\nStarting Task = annotate.ANNOTATE\r\n\u001B[*****************************************************************\r\n*************************ERROR***********************************\r\nDuring annotate, the following command failed with return code 2:\r\n>> /home/prabhakaranra/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/kraken/bin/kraken --threads 15 -db /home/prabhakaranra/metAMOS-1.5rc3/Utilities/DB//kraken /home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig --preload   | kraken-filter --db /home/prabhakaranra/metAMOS-1.5rc3/Utilities/DB//kraken --threshold 0.05 > /home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits\r\n\r\n*************************DETAILS***********************************\r\nLast 10 commands run before the error (/home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Logs/COMMANDS.log)\r\n|2015-04-10 17:26:43| touch /home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Logs/findrepeats.skip\r\n|2015-04-10 17:26:44|# [ANNOTATE]\r\n|2015-04-10 17:26:44| touch /home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.annots\r\n|2015-04-10 17:26:44| unlink /home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig\r\n|2015-04-10 17:26:44| ln /home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Assemble/out/proba.asm.contig /home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig\r\n|2015-04-10 17:26:44| unlink /home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits\r\n|2015-04-10 17:26:44| rm -f /home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Annotate/out/*.hits\r\n|2015-04-10 17:26:44| rm -f /home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Annotate/out/*.epsilon-nb_results.txt\r\n|2015-04-10 17:26:44| rm -f /home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Annotate/out/*.phymm.out\r\n|2015-04-10 17:26:44| /home/prabhakaranra/metAMOS-1.5rc3/Utilities/cpp/Linux-x86_64/kraken/bin/kraken --threads 15 -db /home/prabhakaranra/metAMOS-1.5rc3/Utilities/DB//kraken /home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Annotate/in/proba.asm.contig --preload   | kraken-filter --db /home/prabhakaranra/metAMOS-1.5rc3/Utilities/DB//kraken --threshold 0.05 > /home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits\r\n\r\nLast 10 lines of output (/home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Logs/ANNOTATE.log)\r\nunlink: cannot unlink ‘/home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Annotate/out/proba.hits’: No such file or directory\r\nkraken-filter: can't open nodes file: No such file or directory\r\nkraken: /home/prabhakaranra/metAMOS-1.5rc3/Utilities/DB//kraken/database.kdb does not exist!\r\n\r\nPlease veryify input data and restart MetAMOS. If the problem persists please contact the MetAMOS development team.\r\n*************************ERROR***********************************\r\n*****************************************************************\r\nrm: cannot remove ‘/home/prabhakaranra/metAMOS-1.5rc3/Test/test1/Logs/annotate.ok’: No such file or directory\r\nOops, MetAMOS finished with errors! see text in red above for details.\r\nprabhakaranra@prabhakaranra-P8X58-AS:~/metAMOS-1.5rc3/Test$ \r\n"}}