{"action":"created","issue":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/229","repository_url":"https://api.github.com/repos/COMBINE-lab/salmon","labels_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/229/labels{/name}","comments_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/229/comments","events_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/229/events","html_url":"https://github.com/COMBINE-lab/salmon/issues/229","id":328187991,"node_id":"MDU6SXNzdWUzMjgxODc5OTE=","number":229,"title":"Salmon v0.10.0: Error in function boost::math::digamma<double>(double): numeric overflow]","user":{"login":"knokknok","id":1275796,"node_id":"MDQ6VXNlcjEyNzU3OTY=","avatar_url":"https://avatars1.githubusercontent.com/u/1275796?v=4","gravatar_id":"","url":"https://api.github.com/users/knokknok","html_url":"https://github.com/knokknok","followers_url":"https://api.github.com/users/knokknok/followers","following_url":"https://api.github.com/users/knokknok/following{/other_user}","gists_url":"https://api.github.com/users/knokknok/gists{/gist_id}","starred_url":"https://api.github.com/users/knokknok/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/knokknok/subscriptions","organizations_url":"https://api.github.com/users/knokknok/orgs","repos_url":"https://api.github.com/users/knokknok/repos","events_url":"https://api.github.com/users/knokknok/events{/privacy}","received_events_url":"https://api.github.com/users/knokknok/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":37,"created_at":"2018-05-31T15:31:28Z","updated_at":"2018-05-31T21:50:49Z","closed_at":null,"author_association":"NONE","body":"Sorry, me   (#228) again...\r\nWhile most of my samples seem to work on linux, I got an exception for one of them:\r\n\r\nVersion Info: This is the most recent version of Salmon.\r\n\\#\\#\\# salmon (mapping-based) v0.10.0\r\n\\#\\#\\# [ program ] => salmon\r\n\\#\\#\\# [ command ] => quant\r\n\\#\\#\\# [ index ] => { salmon010.index.all_combined }\r\n\\#\\#\\# [ libType ] => { A }\r\n\\#\\#\\# [ mates1 ] => { R1.fastq.gz }\r\n\\#\\#\\# [ mates2 ] => { R2.fastq.gz }\r\n\\#\\#\\# [ posBias ] => { }\r\n\\#\\#\\# [ gcBias ] => { }\r\n\\#\\#\\# [ seqBias ] => { }\r\n\\#\\#\\# [ useVBOpt ] => { }\r\n\\#\\#\\# [ validateMappings ] => { }\r\n\\#\\#\\# [ output ] => { processed_salmon0100_k31_allcombined/R }\r\nLogs will be written to processed_salmon0100_k31_allcombined/R/logs\r\n[2018-05-31 16:54:42.310] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.\r\n[2018-05-31 16:54:42.310] [jointLog] [info] Usage of --validateMappings implies use of range factorization. rangeFactorizationBins is being set to 4\r\n[2018-05-31 16:54:42.310] [jointLog] [info] parsing read library format\r\n[2018-05-31 16:54:42.310] [jointLog] [info] There is 1 library.\r\n[2018-05-31 16:54:42.480] [jointLog] [info] Loading Quasi index\r\n[2018-05-31 16:54:42.501] [jointLog] [info] Loading 32-bit quasi index\r\n[2018-05-31 16:54:42.501] [stderrLog] [info] Loading Suffix Array\r\n[2018-05-31 16:55:01.293] [stderrLog] [info] Loading Transcript Info\r\n[2018-05-31 16:55:06.428] [stderrLog] [info] Loading Rank-Select Bit Array\r\n[2018-05-31 16:55:07.107] [stderrLog] [info] There were 310732 set bits in the bit array\r\n[2018-05-31 16:55:07.158] [stderrLog] [info] Computing transcript lengths\r\n[2018-05-31 16:55:07.159] [stderrLog] [info] Waiting to finish loading hash\r\n[2018-05-31 16:55:25.973] [jointLog] [info] done\r\n[2018-05-31 16:55:25.973] [jointLog] [info] Index contained 310732 targets\r\n[2018-05-31 16:55:25.973] [stderrLog] [info] Done loading index\r\n\r\nprocessed 67500000 fragmentsointLog] [info] Automatically detected most likely library type as IU\r\nhits: 224580543, hits per frag:  3.35031[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 1.04% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.96% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.84% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.96% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.88% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 1.00% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.92% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.84% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.84% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.86% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.94% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.96% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.98% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.92% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.94% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.98% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.92% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 1.04% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 1.02% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.92% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.92% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.94% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.88% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.90% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.94% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.86% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.86% zero probability fragments\r\n[2018-05-31 17:08:09.486] [jointLog] [info] Thread saw mini-batch with a maximum of 0.86% zero probability fragments\r\n[2018-05-31 17:08:09.498] [jointLog] [info] Thread saw mini-batch with a maximum of 0.90% zero probability fragments\r\n[2018-05-31 17:08:09.534] [jointLog] [info] Thread saw mini-batch with a maximum of 0.90% zero probability fragments\r\n[2018-05-31 17:08:09.572] [jointLog] [info] Thread saw mini-batch with a maximum of 1.04% zero probability fragments\r\n[2018-05-31 17:08:09.634] [jointLog] [info] Thread saw mini-batch with a maximum of 0.90% zero probability fragments\r\n[2018-05-31 17:08:09.641] [jointLog] [info] Thread saw mini-batch with a maximum of 1.00% zero probability fragments\r\n[2018-05-31 17:08:09.649] [jointLog] [info] Thread saw mini-batch with a maximum of 0.88% zero probability fragments\r\n[2018-05-31 17:08:09.690] [jointLog] [info] Thread saw mini-batch with a maximum of 0.96% zero probability fragments\r\n[2018-05-31 17:08:09.702] [jointLog] [info] Thread saw mini-batch with a maximum of 0.92% zero probability fragments\r\n[2018-05-31 17:08:09.721] [jointLog] [info] Thread saw mini-batch with a maximum of 0.88% zero probability fragments\r\n[2018-05-31 17:08:09.728] [jointLog] [info] Thread saw mini-batch with a maximum of 0.90% zero probability fragments\r\n[2018-05-31 17:08:09.782] [jointLog] [info] Thread saw mini-batch with a maximum of 0.86% zero probability fragments\r\n[2018-05-31 17:08:09.786] [jointLog] [info] Thread saw mini-batch with a maximum of 0.90% zero probability fragments\r\n\r\n[2018-05-31 17:08:10.483] [jointLog] [info] Computed 582392 rich equivalence classes for further processing\r\n[2018-05-31 17:08:10.483] [jointLog] [info] Counted 59985194 total reads in the equivalence classes\r\n[2018-05-31 17:08:10.551] [jointLog] [info] Mapping rate = 88.2723%\r\n\r\n[2018-05-31 17:08:10.551] [jointLog] [info] finished quantifyLibrary()\r\n[2018-05-31 17:08:10.551] [jointLog] [info] Starting optimizer\r\n[2018-05-31 17:08:11.488] [jointLog] [info] Marked 1 weighted equivalence classes as degenerate\r\n[2018-05-31 17:08:11.523] [jointLog] [info] iteration = 0 | max rel diff. = 127.399\r\nException : [Error in function boost::math::digamma<double>(double): numeric overflow]\r\nsalmon quant was invoked improperly.\r\nFor usage information, try salmon quant --help\r\nExiting."},"comment":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/comments/393692237","html_url":"https://github.com/COMBINE-lab/salmon/issues/229#issuecomment-393692237","issue_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/229","id":393692237,"node_id":"MDEyOklzc3VlQ29tbWVudDM5MzY5MjIzNw==","user":{"login":"knokknok","id":1275796,"node_id":"MDQ6VXNlcjEyNzU3OTY=","avatar_url":"https://avatars1.githubusercontent.com/u/1275796?v=4","gravatar_id":"","url":"https://api.github.com/users/knokknok","html_url":"https://github.com/knokknok","followers_url":"https://api.github.com/users/knokknok/followers","following_url":"https://api.github.com/users/knokknok/following{/other_user}","gists_url":"https://api.github.com/users/knokknok/gists{/gist_id}","starred_url":"https://api.github.com/users/knokknok/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/knokknok/subscriptions","organizations_url":"https://api.github.com/users/knokknok/orgs","repos_url":"https://api.github.com/users/knokknok/repos","events_url":"https://api.github.com/users/knokknok/events{/privacy}","received_events_url":"https://api.github.com/users/knokknok/received_events","type":"User","site_admin":false},"created_at":"2018-05-31T21:50:49Z","updated_at":"2018-05-31T21:50:49Z","author_association":"NONE","body":"Ok, GMT+2 here, have to go ;-)"}}
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