{"action":"created","issue":{"url":"https://api.github.com/repos/svm-zhang/AGOUTI/issues/7","repository_url":"https://api.github.com/repos/svm-zhang/AGOUTI","labels_url":"https://api.github.com/repos/svm-zhang/AGOUTI/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/svm-zhang/AGOUTI/issues/7/comments","events_url":"https://api.github.com/repos/svm-zhang/AGOUTI/issues/7/events","html_url":"https://github.com/svm-zhang/AGOUTI/issues/7","id":169328598,"number":7,"title":"Error while recovering original scaffolding","user":{"login":"bananenbongo","id":8344880,"avatar_url":"https://avatars.githubusercontent.com/u/8344880?v=3","gravatar_id":"","url":"https://api.github.com/users/bananenbongo","html_url":"https://github.com/bananenbongo","followers_url":"https://api.github.com/users/bananenbongo/followers","following_url":"https://api.github.com/users/bananenbongo/following{/other_user}","gists_url":"https://api.github.com/users/bananenbongo/gists{/gist_id}","starred_url":"https://api.github.com/users/bananenbongo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bananenbongo/subscriptions","organizations_url":"https://api.github.com/users/bananenbongo/orgs","repos_url":"https://api.github.com/users/bananenbongo/repos","events_url":"https://api.github.com/users/bananenbongo/events{/privacy}","received_events_url":"https://api.github.com/users/bananenbongo/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2016-08-04T09:17:31Z","updated_at":"2016-08-04T14:42:58Z","closed_at":null,"body":"Hello again,\r\nafter last times succesful and quick bug handling (again, many thanks!), I've encountered a new error message while trying to recover the original scaffolding after shredding. My workflow is : \r\n```\r\nagouti.py shred -assembly genome.fasta -gff genome.gff -p scaffold\r\n\r\nbwa index -p contigmapping -a bwtsw scaffold.ctg.fasta\r\n\r\nbwa mem -t 80 -T 30 -P -k 20  contigmapping R1_reads.fastq R2_reads.fastq > mapping.ctg.sam\r\n\r\nsamtools view -Sb mapping.ctg.sam > mapping.ctg.bam\r\n\r\npython agouti.py scaffold -assembly scaffold.ctg.fasta -bam mapping.ctg.bam -gff scaffold.ctg.gff -outdir ./run1 -shredpath scaffold.shred.info.txt\r\n```\r\n\r\nThe error i get is \r\n\r\n> 2016-08-04 06:36:27,146 - INFO - AGOUTI_PATH PROGRESS - Analyzing scaffolding paths\r\n2016-08-04 06:36:27,148 - INFO - AGOUTI_PATH PROGRESS - [BEGIN] Reading file with shred info\r\n2016-08-04 06:36:27,931 - ERROR - AGOUTI_PATH PROGRESS - Number of shredded contigs parsed: 242231\r\n2016-08-04 06:36:27,931 - INFO - AGOUTI_PATH PROGRESS - [DONE]\r\n2016-08-04 06:36:27,931 - INFO - AGOUTI_PATH PROGRESS - [BEGIN] Recovring original scaffolding\r\nTraceback (most recent call last):\r\n  File \"agouti.py\", line 283, in <module>\r\n    main()\r\n  File \"agouti.py\", line 280, in main\r\n    args.func(args)\r\n  File \"agouti.py\", line 219, in run_scaffolder\r\n    prefix)\r\n  File \"src/agouti_path.py\", line 38, in agouti_path_main\r\n    agPathDebug)\r\n  File \"src/agouti_path.py\", line 114, in recover_untouched_sequences\r\n    preIndex = int(preGeneID.split('_')[1])\r\nValueError: invalid literal for int() with base 10: 'shred'\r\n\r\n\r\nI'm under the impression it tries to recover unshredded genes from the gff but somehow still gets the shredded ones and therefore has trouble with the ID. My workaround so far is:\r\n\r\n```\r\n`if curCtg in dGFFs:\r\n    curCtgGeneModel5 = dGFFs[curCtg][0]\r\n    if not curCtgGeneModel5.fake:\r\n        curGeneID = curCtgGeneModel5.geneID\r\n        if curGeneID.split('_')[1] != \"shred\":\r\n            curIndex = int(curGeneID.split('_')[1])`\r\n\r\n```\r\nstarting line 116 in agouti_path.py, but the rerun has not reached that phase yet, because it is still graph building. Which brings me to the question, whether there is a way to recover the outcome of \r\n\r\n>  INFO - AGOUTI_SCAFFOLDING PROGRESS - Building graph from joining reads pairs\r\n\r\nfrom a previous run. Hope this is not an error thrown by some stupid mistake in the command line from my side.\r\n\r\nCheers,\r\nNico\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/svm-zhang/AGOUTI/issues/comments/237574595","html_url":"https://github.com/svm-zhang/AGOUTI/issues/7#issuecomment-237574595","issue_url":"https://api.github.com/repos/svm-zhang/AGOUTI/issues/7","id":237574595,"user":{"login":"bananenbongo","id":8344880,"avatar_url":"https://avatars.githubusercontent.com/u/8344880?v=3","gravatar_id":"","url":"https://api.github.com/users/bananenbongo","html_url":"https://github.com/bananenbongo","followers_url":"https://api.github.com/users/bananenbongo/followers","following_url":"https://api.github.com/users/bananenbongo/following{/other_user}","gists_url":"https://api.github.com/users/bananenbongo/gists{/gist_id}","starred_url":"https://api.github.com/users/bananenbongo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bananenbongo/subscriptions","organizations_url":"https://api.github.com/users/bananenbongo/orgs","repos_url":"https://api.github.com/users/bananenbongo/repos","events_url":"https://api.github.com/users/bananenbongo/events{/privacy}","received_events_url":"https://api.github.com/users/bananenbongo/received_events","type":"User","site_admin":false},"created_at":"2016-08-04T14:42:58Z","updated_at":"2016-08-04T14:42:58Z","body":"yep. restartign job right now with the newest version. Will let you know how it goes"}}
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