{"action":"created","issue":{"url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/393","repository_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq","labels_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/393/labels{/name}","comments_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/393/comments","events_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/393/events","html_url":"https://github.com/trinityrnaseq/trinityrnaseq/issues/393","id":292809559,"number":393,"title":"GOseq error:","user":{"login":"luca-peruz","id":34270780,"avatar_url":"https://avatars1.githubusercontent.com/u/34270780?v=4","gravatar_id":"","url":"https://api.github.com/users/luca-peruz","html_url":"https://github.com/luca-peruz","followers_url":"https://api.github.com/users/luca-peruz/followers","following_url":"https://api.github.com/users/luca-peruz/following{/other_user}","gists_url":"https://api.github.com/users/luca-peruz/gists{/gist_id}","starred_url":"https://api.github.com/users/luca-peruz/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/luca-peruz/subscriptions","organizations_url":"https://api.github.com/users/luca-peruz/orgs","repos_url":"https://api.github.com/users/luca-peruz/repos","events_url":"https://api.github.com/users/luca-peruz/events{/privacy}","received_events_url":"https://api.github.com/users/luca-peruz/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":15,"created_at":"2018-01-30T14:48:10Z","updated_at":"2018-02-13T14:39:55Z","closed_at":null,"author_association":"NONE","body":"Hi everyone. I was running the GOseq utility to perform gene ontology functional enrichment tests. The code was running fine until I got this error message, and I was hoping someone could help with it?\r\nThanks in advance for your help. \r\nLuca\r\n\r\n\r\nThe code was running this command when the error happened:\r\n\r\n> #organize go_id -> list of genes\r\n> GO_to_gene_list = list()\r\n> for (gene_id in names(GO_info_listed)) {\r\n+     go_list = GO_info_listed[[gene_id]]\r\n+     for (go_id in go_list) {\r\n+         GO_to_gene_list[[go_id]] = c(GO_to_gene_list[[go_id]], gene_id)\r\n+     }\r\n+ }\r\n\r\nError:\r\n`sh: line 1:  5195 Killed                  R --no-save --no-restore --no-site-file --no-init-file --quiet < __runGOseq.R\r\nError, cmd: R --no-save --no-restore --no-site-file --no-init-file --quiet < __runGOseq.R died with ret 35072 at /home/local/software/trinity/trinityrnaseq-Trinity-v2.4.0/Analysis/DifferentialExpression/run_GOseq.pl line 196.\r\nError, cmd: /home/local/software/trinity/trinityrnaseq-Trinity-v2.4.0/Analysis/DifferentialExpression/run_GOseq.pl --GO_assignments ../../annotation_trinotate/Trinotate_annotation_report.complete.xls.gene_ontology  --lengths ../../annotation_trinotate/Trinity.18h.seqLenghts --genes_single_factor Trinity_trans.counts.matrix.Control_vs_Infected.edgeR.DE_results.P1e-3_C2.Control-UP.subset --background Trinity_trans.counts.matrix.Control_vs_Infected.edgeR.count_matrix  died with ret 6400 at /local/software/trinity/trinityrnaseq-Trinity-v2.4.0/Analysis/DifferentialExpression/analyze_diff_expr.pl line 272.`\r\n\r\nInitial command used:\r\n\r\n`/local/software/trinity/trinityrnaseq-Trinity-v2.4.0/Analysis/DifferentialExpression/analyze_diff_expr.pl \\\r\n--matrix ../../expression_levels.kmer1/Trinity_trans.TMM.EXPR.matrix \\  \r\n--examine_GO_enrichment \\\r\n--GO_annots ../../annotation_trinotate/Trinotate_annotation_report.complete.xls.gene_ontology \\\r\n--gene_lengths ../../annotation_trinotate/Trinity.18h.seqLenghts \\\r\n--samples ../samples.txt -P 1e-3 -C 2`"},"comment":{"url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/comments/365285870","html_url":"https://github.com/trinityrnaseq/trinityrnaseq/issues/393#issuecomment-365285870","issue_url":"https://api.github.com/repos/trinityrnaseq/trinityrnaseq/issues/393","id":365285870,"user":{"login":"brianjohnhaas","id":7542111,"avatar_url":"https://avatars0.githubusercontent.com/u/7542111?v=4","gravatar_id":"","url":"https://api.github.com/users/brianjohnhaas","html_url":"https://github.com/brianjohnhaas","followers_url":"https://api.github.com/users/brianjohnhaas/followers","following_url":"https://api.github.com/users/brianjohnhaas/following{/other_user}","gists_url":"https://api.github.com/users/brianjohnhaas/gists{/gist_id}","starred_url":"https://api.github.com/users/brianjohnhaas/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/brianjohnhaas/subscriptions","organizations_url":"https://api.github.com/users/brianjohnhaas/orgs","repos_url":"https://api.github.com/users/brianjohnhaas/repos","events_url":"https://api.github.com/users/brianjohnhaas/events{/privacy}","received_events_url":"https://api.github.com/users/brianjohnhaas/received_events","type":"User","site_admin":false},"created_at":"2018-02-13T14:39:55Z","updated_at":"2018-02-13T14:39:55Z","author_association":"OWNER","body":"I agree it would be useful for that to work.   It probably requires some\nmore coding and app refinement as opposed to tweaking the data loading.\n It'll have to go on the list.  I need a helper here. ;-)\n\n~b\n\nOn Tue, Feb 13, 2018 at 9:34 AM, luca-peruz <notifications@github.com>\nwrote:\n\n> Thanks Brian! I would love to help but I don’t know how to do it…\n> An additional question, on Trinotate Web, I was trying to insert\n> annotations so that in the DE analysis I can “filter” by using a specific\n> annotation… But I always end up without annotations in the volcano plots\n> even if I can search for annotations (in the “annotation keyword search”)\n> and it works… I updated the count matrix and TMM matrix with the\n> annotations, and I loaded into the sqlite database, but it does not work…\n> Any suggestions?\n> Thanks\n> Luca\n>\n> From: Brian Haas <notifications@github.com>\n> Reply-To: trinityrnaseq/trinityrnaseq <reply@reply.github.com>\n> Date: Tuesday, 13 February 2018 at 14:26\n> To: trinityrnaseq/trinityrnaseq <trinityrnaseq@noreply.github.com>\n> Cc: \"Peruzza L.\" <Luca.Peruzza@soton.ac.uk>, Author <\n> author@noreply.github.com>\n> Subject: Re: [trinityrnaseq/trinityrnaseq] GOseq error: (#393)\n>\n> great!\n>\n> The GO stuff doesn't get loaded back into Trinotate for use w/\n> TrinotateWeb\n> yet. I'm planning to do this at some point, but too many other priorities\n> at the moment. If anyone wants to volunteer to work on it, that would be\n> welcomed!\n>\n> ~b\n>\n> On Tue, Feb 13, 2018 at 9:20 AM, luca-peruz <notifications@github.com>\n> wrote:\n>\n> > Dear Brian,\n> > I managed to solve the issue. I was using a version of goseq that had\n> the\n> > option \"use_genes_without_cat = TRUE\" by default. Newer versions of it\n> have\n> > it to false by default. Using a newer version of goseq, solved the\n> issue!\n> >\n> > Is there a way to load the results into Trinotate Web?\n> > Thanks again\n> > Luca\n> >\n> > —\n> > You are receiving this because you commented.\n> > Reply to this email directly, view it on GitHub\n> > <https://github.com/trinityrnaseq/trinityrnaseq/issues/393#issuecomment-\n> 365280216>,\n> > or mute the thread\n> > <https://github.com/notifications/unsubscribe-auth/AHMVX_\n> bjuZJGPfcjLP8LbN424we_bXDnks5tUZozgaJpZM4RycmO>\n> > .\n> >\n>\n>\n>\n> --\n> --\n> Brian J. Haas\n> The Broad Institute\n> http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>\n>\n>\n> —\n> You are receiving this because you authored the thread.\n> Reply to this email directly, view it on GitHub<https://github.com/\n> trinityrnaseq/trinityrnaseq/issues/393#issuecomment-365281607>, or mute\n> the thread<https://github.com/notifications/unsubscribe-auth/\n> AgruPKSnDY5mKM0obRJLxd3sFwhIdxN1ks5tUZtIgaJpZM4RycmO>.\n>\n> —\n> You are receiving this because you commented.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/trinityrnaseq/trinityrnaseq/issues/393#issuecomment-365284163>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AHMVX9-Gc3ByMZ_BLRu0I8zsgBkdeV2hks5tUZ1dgaJpZM4RycmO>\n> .\n>\n\n\n\n-- \n--\nBrian J. Haas\nThe Broad Institute\nhttp://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>\n"}}
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