{"action":"created","issue":{"url":"https://api.github.com/repos/erhard-lab/price/issues/7","repository_url":"https://api.github.com/repos/erhard-lab/price","labels_url":"https://api.github.com/repos/erhard-lab/price/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/erhard-lab/price/issues/7/comments","events_url":"https://api.github.com/repos/erhard-lab/price/issues/7/events","html_url":"https://github.com/erhard-lab/price/issues/7","id":310465078,"number":7,"title":"Error while running Price","user":{"login":"antonvila","id":7216964,"avatar_url":"https://avatars3.githubusercontent.com/u/7216964?v=4","gravatar_id":"","url":"https://api.github.com/users/antonvila","html_url":"https://github.com/antonvila","followers_url":"https://api.github.com/users/antonvila/followers","following_url":"https://api.github.com/users/antonvila/following{/other_user}","gists_url":"https://api.github.com/users/antonvila/gists{/gist_id}","starred_url":"https://api.github.com/users/antonvila/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/antonvila/subscriptions","organizations_url":"https://api.github.com/users/antonvila/orgs","repos_url":"https://api.github.com/users/antonvila/repos","events_url":"https://api.github.com/users/antonvila/events{/privacy}","received_events_url":"https://api.github.com/users/antonvila/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-04-02T11:44:44Z","updated_at":"2018-04-03T07:26:55Z","closed_at":null,"author_association":"NONE","body":"Dear Florian,\r\n\r\nI successfully installed Price and all the dependencies and performed the tests with the supplied dataset. While attempting to run Price with my data I got the following error:\r\n\r\n2018-04-02 13:34:23.430 INFO Command: gedi -e Price -reads /media/anton/Maxtor/AVS/DATA/A549_RP_mitochondrial/RP_01JUL2015_DEN2_REP1_mitochondrial_032417_sorted.bam -genomic Homo_sapiens_GRCh38_MT -prefix RP_01JUL2015_DEN2_REP1\r\n2018-04-02 13:34:23.566 INFO Discovering classes in classpath\r\n2018-04-02 13:34:23.693 INFO Preparing simple class references\r\n2018-04-02 13:34:23.821 INFO Gedi 1.0.2 (JAR) startup\r\n2018-04-02 13:34:23.928 INFO Reading oml /home/anton/.gedi/genomic/Homo_sapiens_GRCh38_MT.oml\r\n2018-04-02 13:34:23.946 INFO Done reading oml /home/anton/.gedi/genomic/Homo_sapiens_GRCh38_MT.oml\r\n2018-04-02 13:34:24.090 INFO Estimating maxpos...\r\n2018-04-02 13:34:24.109 INFO Clustering reads\r\n2018-04-02 13:34:32.416 INFO Found 230 clusters without looking at annotation\r\n2018-04-02 13:34:32.428 INFO Found 9 clusters after looking at annotation\r\n2018-04-02 13:34:32.434 INFO Found 5 clusters after filtering with read/region count\r\nPRICE\r\nPRICE is an analysis method for Ribo-seq data.\r\n\r\nError:\r\njava.lang.RuntimeException: Could not run gedi.riboseq.javapipeline.PriceEstimateModel@72d8e628\r\nCould not run gedi.riboseq.javapipeline.PriceEstimateModel@72d8e628\r\n0\r\n\r\ngedi -e PRICE <Options>\r\n\r\nGeneral:\r\n -reads <reads>        The mapped reads from the ribo-seq experiment.\r\n -prefix <prefix>      The prefix used for all output files\r\n -genomic <genomic>    The indexed GEDI genome.\r\n\r\nCommandline:\r\n -progress             Show progress\r\n -D                    Verbose output of errors\r\n -h                    Show usage\r\n -hh                   Show verbose usage\r\n -hhh                  Show extra verbose usage\r\n -dry                  Dry run\r\n -keep                 Do not remove temp files\r\n\r\nany ideas of what might be wrong?\r\n\r\nbest,\r\n\r\nAntón"},"comment":{"url":"https://api.github.com/repos/erhard-lab/price/issues/comments/378154569","html_url":"https://github.com/erhard-lab/price/issues/7#issuecomment-378154569","issue_url":"https://api.github.com/repos/erhard-lab/price/issues/7","id":378154569,"user":{"login":"florianerhard","id":16842287,"avatar_url":"https://avatars1.githubusercontent.com/u/16842287?v=4","gravatar_id":"","url":"https://api.github.com/users/florianerhard","html_url":"https://github.com/florianerhard","followers_url":"https://api.github.com/users/florianerhard/followers","following_url":"https://api.github.com/users/florianerhard/following{/other_user}","gists_url":"https://api.github.com/users/florianerhard/gists{/gist_id}","starred_url":"https://api.github.com/users/florianerhard/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/florianerhard/subscriptions","organizations_url":"https://api.github.com/users/florianerhard/orgs","repos_url":"https://api.github.com/users/florianerhard/repos","events_url":"https://api.github.com/users/florianerhard/events{/privacy}","received_events_url":"https://api.github.com/users/florianerhard/received_events","type":"User","site_admin":false},"created_at":"2018-04-03T07:26:55Z","updated_at":"2018-04-03T07:26:55Z","author_association":"CONTRIBUTOR","body":"Hi Anton,\r\n\r\ncould you try running it with the `-D` flag, which gives a more verbose output of errors!\r\n\r\nFrom the output, 5 clusters seem quite few. Are you trying to run price on a subset (mitochondrial only, as suggested by filenames) of all reads? I would advice against that, as to build an accurate codon model, price needs many reads! \r\n\r\nBest,\r\nFlorian"}}
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