{"action":"created","issue":{"url":"https://api.github.com/repos/pachterlab/sleuth/issues/175","repository_url":"https://api.github.com/repos/pachterlab/sleuth","labels_url":"https://api.github.com/repos/pachterlab/sleuth/issues/175/labels{/name}","comments_url":"https://api.github.com/repos/pachterlab/sleuth/issues/175/comments","events_url":"https://api.github.com/repos/pachterlab/sleuth/issues/175/events","html_url":"https://github.com/pachterlab/sleuth/issues/175","id":326665228,"node_id":"MDU6SXNzdWUzMjY2NjUyMjg=","number":175,"title":"sleuth_prep() yields subscript out of bounds error","user":{"login":"channsoden","id":13953331,"node_id":"MDQ6VXNlcjEzOTUzMzMx","avatar_url":"https://avatars3.githubusercontent.com/u/13953331?v=4","gravatar_id":"","url":"https://api.github.com/users/channsoden","html_url":"https://github.com/channsoden","followers_url":"https://api.github.com/users/channsoden/followers","following_url":"https://api.github.com/users/channsoden/following{/other_user}","gists_url":"https://api.github.com/users/channsoden/gists{/gist_id}","starred_url":"https://api.github.com/users/channsoden/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/channsoden/subscriptions","organizations_url":"https://api.github.com/users/channsoden/orgs","repos_url":"https://api.github.com/users/channsoden/repos","events_url":"https://api.github.com/users/channsoden/events{/privacy}","received_events_url":"https://api.github.com/users/channsoden/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":22,"created_at":"2018-05-25T21:11:15Z","updated_at":"2018-06-08T23:50:34Z","closed_at":null,"author_association":"NONE","body":"sleuth_prep seems to always error with \"subscript out of bounds\" during step \"normalizing est_counts\". I'm trying this on my own data since, as others have pointed out, the link to the sample data is broken.\r\n\r\n```\r\ndesign <- read.table(file.path(\".\", \"metadata_table.tsv\"),\r\n                      header = TRUE,\r\n                      stringsAsFactors=FALSE)\r\ns2c <- dplyr::select(design, sample, condition = carbon, path)\r\ns2c\r\n\r\nsample | condition | path\r\n-- | -- | --\r\nMM10_16C_L_wt | L | wt/MM10_16C_L_corrected_kallisto\r\nMM10_16C_R_wt | R | wt/MM10_16C_R_corrected_kallisto\r\nMM10_22C_L_wt | L | wt/MM10_22C_L_corrected_kallisto\r\nMM10_22C_R_wt | R | wt/MM10_22C_R_corrected_kallisto\r\nMM18_16C_L_wt | L | wt/MM18_16C_L_corrected_kallisto\r\nMM18_16C_R_wt | R | wt/MM18_16C_R_corrected_kallisto\r\nMM18_22C_L_wt | L | wt/MM18_22C_L_1_corrected_kallisto\r\nMM18_22C_L_wt | L | wt/MM18_22C_L_2_corrected_kallisto\r\nMM18_22C_L_wt | L | wt/MM18_22C_L_3_corrected_kallisto\r\nMM18_22C_L_wt | L | wt/MM18_22C_L_corrected_kallisto\r\nMM18_22C_R_wt | R | wt/MM18_22C_R_corrected_kallisto\r\nMM20_16C_L_wt | L | wt/MM20_16C_L_corrected_kallisto\r\nMM20_16C_R_wt | R | wt/MM20_16C_R_corrected_kallisto\r\nMM20_22C_L_wt | L | wt/MM20_22C_L_corrected_kallisto\r\n...\r\n\r\nso <- sleuth_prep(s2c, extra_bootstrap_summary = TRUE)\r\n\r\nreading in kallisto results\r\ndropping unused factor levels\r\n..............................................................................................\r\nnormalizing est_counts\r\nError in result[, which_order, drop = FALSE]: subscript out of bounds\r\nTraceback:\r\n\r\n1. sleuth_prep(s2c, extra_bootstrap_summary = TRUE)\r\n2. spread_abundance_by(obs_raw, \"est_counts\", sample_to_covariates$sample)\r\n```\r\n\r\nAny advice on troubleshooting this?"},"comment":{"url":"https://api.github.com/repos/pachterlab/sleuth/issues/comments/395920991","html_url":"https://github.com/pachterlab/sleuth/issues/175#issuecomment-395920991","issue_url":"https://api.github.com/repos/pachterlab/sleuth/issues/175","id":395920991,"node_id":"MDEyOklzc3VlQ29tbWVudDM5NTkyMDk5MQ==","user":{"login":"warrenmcg","id":6866073,"node_id":"MDQ6VXNlcjY4NjYwNzM=","avatar_url":"https://avatars1.githubusercontent.com/u/6866073?v=4","gravatar_id":"","url":"https://api.github.com/users/warrenmcg","html_url":"https://github.com/warrenmcg","followers_url":"https://api.github.com/users/warrenmcg/followers","following_url":"https://api.github.com/users/warrenmcg/following{/other_user}","gists_url":"https://api.github.com/users/warrenmcg/gists{/gist_id}","starred_url":"https://api.github.com/users/warrenmcg/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/warrenmcg/subscriptions","organizations_url":"https://api.github.com/users/warrenmcg/orgs","repos_url":"https://api.github.com/users/warrenmcg/repos","events_url":"https://api.github.com/users/warrenmcg/events{/privacy}","received_events_url":"https://api.github.com/users/warrenmcg/received_events","type":"User","site_admin":false},"created_at":"2018-06-08T23:50:34Z","updated_at":"2018-06-08T23:50:34Z","author_association":"COLLABORATOR","body":"rhdf5 installs its own internally, so we either would have to ask the developer there to switch the package to hdf5 lib 1.10, or you would need to install the older version of hdf5 lib on your machine (1.8.x). What I don’t know is whether it works to have both versions on your machine and which kallisto will use. If you’re comfortable experimenting, that would be the next step.\r\n\r\n@pimentel, from our end, I think the best thing to do is open an issue in kallisto to see if the hdf5 lib version can be included either in the h5 files themselves or the run info json file. It would also be worth it to include a warning of hdf5 lib is version 1.10, since it can’t currently be processed by sleuth. Then, sleuth could do a check to make sure that the rhdf5 internal hdf5 lib version is compatible with the version used by kallisto."}}
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