{"action":"created","issue":{"url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/98","repository_url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit","labels_url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/98/labels{/name}","comments_url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/98/comments","events_url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/98/events","html_url":"https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/98","id":330978050,"node_id":"MDU6SXNzdWUzMzA5NzgwNTA=","number":98,"title":"mis-formatted hints file","user":{"login":"nbedelman","id":13751276,"node_id":"MDQ6VXNlcjEzNzUxMjc2","avatar_url":"https://avatars3.githubusercontent.com/u/13751276?v=4","gravatar_id":"","url":"https://api.github.com/users/nbedelman","html_url":"https://github.com/nbedelman","followers_url":"https://api.github.com/users/nbedelman/followers","following_url":"https://api.github.com/users/nbedelman/following{/other_user}","gists_url":"https://api.github.com/users/nbedelman/gists{/gist_id}","starred_url":"https://api.github.com/users/nbedelman/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nbedelman/subscriptions","organizations_url":"https://api.github.com/users/nbedelman/orgs","repos_url":"https://api.github.com/users/nbedelman/repos","events_url":"https://api.github.com/users/nbedelman/events{/privacy}","received_events_url":"https://api.github.com/users/nbedelman/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-06-10T15:30:43Z","updated_at":"2018-06-12T15:23:46Z","closed_at":null,"author_association":"NONE","body":"I'm running into a seemingly minor issue with the first augustus step in the pipeline. I get the error below:\r\n\r\n```\r\n2018-06-10 11:15:24,717 - toil.leader - WARNING - 5/v/job9c1JLI    ---TOIL WORKER OUTPUT LOG---\r\n2018-06-10 11:15:24,717 - toil.leader - WARNING - 5/v/job9c1JLI    INFO:toil:Running Toil version 3.13.0a1.\r\n2018-06-10 11:15:24,718 - toil.leader - WARNING - 5/v/job9c1JLI    WARNING:toil.resource:Can't find resource for leader path '/n/mallet_lab/edelman/software/Comparative-Annotation-Toolkit/cat'\r\n2018-06-10 11:15:24,718 - toil.leader - WARNING - 5/v/job9c1JLI    WARNING:toil.resource:Can't localize module ModuleDescriptor(dirPath='/n/mallet_lab/edelman/software/Comparative-Annotation-Toolkit', name='cat.augustus', fromVirtualEnv=False)\r\n2018-06-10 11:15:24,718 - toil.leader - WARNING - 5/v/job9c1JLI    WARNING:toil.resource:Can't find resource for leader path '/n/mallet_lab/edelman/software/Comparative-Annotation-Toolkit/cat'\r\n2018-06-10 11:15:24,718 - toil.leader - WARNING - 5/v/job9c1JLI    WARNING:toil.resource:Can't localize module ModuleDescriptor(dirPath='/n/mallet_lab/edelman/software/Comparative-Annotation-Toolkit', name='cat.augustus', fromVirtualEnv=False)\r\n2018-06-10 11:15:24,719 - toil.leader - WARNING - 5/v/job9c1JLI    Traceback (most recent call last):\r\n2018-06-10 11:15:24,719 - toil.leader - WARNING - 5/v/job9c1JLI      File \"/n/home09/nedelman/.conda/envs/CAT/lib/python2.7/site-packages/toil/worker.py\", line 316, in main\r\n2018-06-10 11:15:24,719 - toil.leader - WARNING - 5/v/job9c1JLI        job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore)\r\n2018-06-10 11:15:24,719 - toil.leader - WARNING - 5/v/job9c1JLI      File \"/n/home09/nedelman/.conda/envs/CAT/lib/python2.7/site-packages/toil/job.py\", line 1318, in _runner\r\n2018-06-10 11:15:24,720 - toil.leader - WARNING - 5/v/job9c1JLI        returnValues = self._run(jobGraph, fileStore)\r\n2018-06-10 11:15:24,720 - toil.leader - WARNING - 5/v/job9c1JLI      File \"/n/home09/nedelman/.conda/envs/CAT/lib/python2.7/site-packages/toil/job.py\", line 1263, in _run\r\n2018-06-10 11:15:24,736 - toil.leader - WARNING - 5/v/job9c1JLI        return self.run(fileStore)\r\n2018-06-10 11:15:24,737 - toil.leader - WARNING - 5/v/job9c1JLI      File \"/n/home09/nedelman/.conda/envs/CAT/lib/python2.7/site-packages/toil/job.py\", line 1447, in run\r\n2018-06-10 11:15:24,737 - toil.leader - WARNING - 5/v/job9c1JLI        rValue = userFunction(*((self,) + tuple(self._args)), **self._kwargs)\r\n2018-06-10 11:15:24,738 - toil.leader - WARNING - 5/v/job9c1JLI      File \"/n/mallet_lab/edelman/software/Comparative-Annotation-Toolkit/cat/augustus.py\", line 141, in run_augustus_chunk\r\n2018-06-10 11:15:24,738 - toil.leader - WARNING - 5/v/job9c1JLI        args.utr)\r\n2018-06-10 11:15:24,738 - toil.leader - WARNING - 5/v/job9c1JLI      File \"/n/mallet_lab/edelman/software/Comparative-Annotation-Toolkit/cat/augustus.py\", line 170, in run_augustus\r\n2018-06-10 11:15:24,738 - toil.leader - WARNING - 5/v/job9c1JLI        aug_output = tools.procOps.call_proc_lines(cmd)\r\n2018-06-10 11:15:24,739 - toil.leader - WARNING - 5/v/job9c1JLI      File \"/n/mallet_lab/edelman/software/Comparative-Annotation-Toolkit/tools/procOps.py\", line 26, in call_proc_lines\r\n2018-06-10 11:15:24,739 - toil.leader - WARNING - 5/v/job9c1JLI        out = call_proc(cmd)\r\n2018-06-10 11:15:24,739 - toil.leader - WARNING - 5/v/job9c1JLI      File \"/n/mallet_lab/edelman/software/Comparative-Annotation-Toolkit/tools/procOps.py\", line 16, in call_proc\r\n2018-06-10 11:15:24,739 - toil.leader - WARNING - 5/v/job9c1JLI        pl.wait()\r\n2018-06-10 11:15:24,739 - toil.leader - WARNING - 5/v/job9c1JLI      File \"/n/mallet_lab/edelman/software/Comparative-Annotation-Toolkit/tools/pipeline.py\", line 1127, in wait\r\n2018-06-10 11:15:24,740 - toil.leader - WARNING - 5/v/job9c1JLI        self.raiseIfExcept()\r\n2018-06-10 11:15:24,740 - toil.leader - WARNING - 5/v/job9c1JLI      File \"/n/mallet_lab/edelman/software/Comparative-Annotation-Toolkit/tools/pipeline.py\", line 1085, in raiseIfExcept\r\n2018-06-10 11:15:24,740 - toil.leader - WARNING - 5/v/job9c1JLI        p.raiseIfExcept()\r\n2018-06-10 11:15:24,740 - toil.leader - WARNING - 5/v/job9c1JLI      File \"/n/mallet_lab/edelman/software/Comparative-Annotation-Toolkit/tools/pipeline.py\", line 749, in raiseIfExcept\r\n2018-06-10 11:15:24,741 - toil.leader - WARNING - 5/v/job9c1JLI        raise self.exceptInfo[0], self.exceptInfo[1], self.exceptInfo[2]\r\n2018-06-10 11:15:24,741 - toil.leader - WARNING - 5/v/job9c1JLI    ProcException: process exited 1: augustus /n/regal/mallet_lab/edelman/18Genomes/results/annotation/heliconiiniAlignment/CAT_annotationsOnly/toil-58bc7781-2b91-42cb-a716-25e18785266b-6b90140c-c47d-4883-96bb-c63ecfe4fd86/tmpA5eHvY/12d86d33-cdc8-4524-932c-39cad14b7734/holy2a08306.rc.fas.harvard.edu.38371.5261701051.tmp --predictionStart=-0 --predictionEnd=-0 --extrinsicCfgFile=/n/regal/mallet_lab/edelman/18Genomes/results/annotation/heliconiiniAlignment/CAT_annotationsOnly/toil-58bc7781-2b91-42cb-a716-25e18785266b-6b90140c-c47d-4883-96bb-c63ecfe4fd86/tmpA5eHvY/12d86d33-cdc8-4524-932c-39cad14b7734/tmpO9nNov.tmp --hintsfile=/n/regal/mallet_lab/edelman/18Genomes/results/annotation/heliconiiniAlignment/CAT_annotationsOnly/toil-58bc7781-2b91-42cb-a716-25e18785266b-6b90140c-c47d-4883-96bb-c63ecfe4fd86/tmpA5eHvY/12d86d33-cdc8-4524-932c-39cad14b7734/holy2a08306.rc.fas.harvard.edu.38371.4639986974.tmp --UTR=0 --alternatives-from-evidence=0 --species=heliconius_melpomene1 --allow_hinted_splicesites=atac --protein=0 --softmasking=1\r\n\r\n```\r\n\r\nAnd when I run the augustus command listed, I get the following output:\r\n\r\n```\r\n# This output was generated with AUGUSTUS (version 3.3).\r\n# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),\r\n# O. Keller, S. König, L. Gerischer and L. Romoth.\r\n# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),\r\n# Using native and syntenically mapped cDNA alignments to improve de novo gene finding\r\n# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013\r\n# Sources of extrinsic information: M RM E W T PB \r\n# Setting individual_liability for T.\r\n# Setting acceptor splice site local malus: 0.1\r\n# Setting donor splice site local malus: 0.1\r\n# Setting exon local malus: 0.98\r\n# Setting CDSpart local malus: 0.98\r\n# Setting UTRpart local malus: 0.98\r\n# reading in the file /n/regal/mallet_lab/edelman/18Genomes/results/annotation/heliconiiniAlignment/CAT_annotationsOnly/toil-58bc7781-2b91-42cb-a716-25e18785266b-6b90140c-c47d-4883-96bb-c63ecfe4fd86/tmpA5eHvY/12d86d33-cdc8-4524-932c-39cad14b7734/holy2a08306.rc.fas.harvard.edu.38371.4639986974.tmp ...\r\nError in hint line: line 1\r\nLine not tab separated.\r\nMaybe you used spaces instead of tabulators?\r\nFeatureCollection::esource: invalid source key: ?\r\n\r\naugustus: ERROR\r\n\tFeatureCollection::esource: invalid source key: ?\r\n```\r\n\r\nI took a look at the \r\n[hintsFile](https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/files/2087990/hintsFile.txt), and the first line just says 'line 1'. If I remove that line and run the command again it works fine. Do you know why it's adding that line, or if there's an easy way to get rid of it? Thanks!\r\n\r\nNate\r\n\r\nPS congrats on the Science paper!\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/comments/396630054","html_url":"https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/98#issuecomment-396630054","issue_url":"https://api.github.com/repos/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit/issues/98","id":396630054,"node_id":"MDEyOklzc3VlQ29tbWVudDM5NjYzMDA1NA==","user":{"login":"ifiddes","id":7818077,"node_id":"MDQ6VXNlcjc4MTgwNzc=","avatar_url":"https://avatars2.githubusercontent.com/u/7818077?v=4","gravatar_id":"","url":"https://api.github.com/users/ifiddes","html_url":"https://github.com/ifiddes","followers_url":"https://api.github.com/users/ifiddes/followers","following_url":"https://api.github.com/users/ifiddes/following{/other_user}","gists_url":"https://api.github.com/users/ifiddes/gists{/gist_id}","starred_url":"https://api.github.com/users/ifiddes/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ifiddes/subscriptions","organizations_url":"https://api.github.com/users/ifiddes/orgs","repos_url":"https://api.github.com/users/ifiddes/repos","events_url":"https://api.github.com/users/ifiddes/events{/privacy}","received_events_url":"https://api.github.com/users/ifiddes/received_events","type":"User","site_admin":false},"created_at":"2018-06-12T15:23:46Z","updated_at":"2018-06-12T15:23:46Z","author_association":"CONTRIBUTOR","body":"Looking at the `grp` key, I am inferring you are passing previously assembled AUGUSTUS transcripts to the protein hints step. Is that correct?\r\n\r\nThis may be a result of behavior change of `pslCheck`... I will look into it. I really should swap genewise or something of that sort in for BLAT in that mode.\r\n\r\nIf you trust your transcripts, I would suggest submitting them to CAT as ANNOTATION instead of PROTEIN_FASTA. This will require you to have them in a GFF3 format that `gff3ToGenePred` can parse, but you don't actually need all of the extra biotype tags if it isn't the reference genome."}}
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