{"action":"created","issue":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/111","repository_url":"https://api.github.com/repos/COMBINE-lab/salmon","labels_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/111/labels{/name}","comments_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/111/comments","events_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/111/events","html_url":"https://github.com/COMBINE-lab/salmon/issues/111","id":195391208,"number":111,"title":"Gibbs sampler hangs forever on one of my samples","user":{"login":"DarwinAwardWinner","id":228145,"avatar_url":"https://avatars.githubusercontent.com/u/228145?v=3","gravatar_id":"","url":"https://api.github.com/users/DarwinAwardWinner","html_url":"https://github.com/DarwinAwardWinner","followers_url":"https://api.github.com/users/DarwinAwardWinner/followers","following_url":"https://api.github.com/users/DarwinAwardWinner/following{/other_user}","gists_url":"https://api.github.com/users/DarwinAwardWinner/gists{/gist_id}","starred_url":"https://api.github.com/users/DarwinAwardWinner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DarwinAwardWinner/subscriptions","organizations_url":"https://api.github.com/users/DarwinAwardWinner/orgs","repos_url":"https://api.github.com/users/DarwinAwardWinner/repos","events_url":"https://api.github.com/users/DarwinAwardWinner/events{/privacy}","received_events_url":"https://api.github.com/users/DarwinAwardWinner/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2016-12-13T22:47:16Z","updated_at":"2016-12-14T00:36:34Z","closed_at":null,"body":"One of my samples seems to be giving Salmon's Gibbs sampler some trouble:\r\n\r\n```\r\n$ salmon quant --index /home/ryan/references/hg38/Salmon_index_hg38.analysisSet_knownGene --unmatedReads fastq_files/SRR2454059.fq.gz --threads 8 --libType ISF --seqBias --gcBias --useVBOpt --dumpEq --dumpEqWeights --geneMap /home/ryan/references/hg38/Salmon_index_hg38.analysisSet_knownGene/genemap.txt --output salmon_quant/hg38.analysisSet_knownGene/SRR2454059 --auxDir aux_info --numGibbsSamples 100\r\nVersion Info: This is the most recent **development version** of Salmon.\r\n### salmon (mapping-based) v0.7.3\r\n### [ program ] => salmon \r\n### [ command ] => quant \r\n### [ index ] => { /home/ryan/references/hg38/Salmon_index_hg38.analysisSet_knownGene }\r\n### [ unmatedReads ] => { fastq_files/SRR2454059.fq.gz }\r\n### [ threads ] => { 8 }\r\n### [ libType ] => { ISF }\r\n### [ seqBias ] => { }\r\n### [ gcBias ] => { }\r\n### [ useVBOpt ] => { }\r\n### [ dumpEq ] => { }\r\n### [ dumpEqWeights ] => { }\r\n### [ geneMap ] => { /home/ryan/references/hg38/Salmon_index_hg38.analysisSet_knownGene/genemap.txt }\r\n### [ output ] => { salmon_quant/hg38.analysisSet_knownGene/SRR2454059 }\r\n### [ auxDir ] => { aux_info }\r\n### [ numGibbsSamples ] => { 100 }\r\nLogs will be written to salmon_quant/hg38.analysisSet_knownGene/SRR2454059/logs\r\n[2016-12-13 12:44:39.271] [jointLog] [info] parsing read library format\r\n[2016-12-13 12:44:39.271] [jointLog] [info] There is 1 library.\r\n[2016-12-13 12:44:39.836] [jointLog] [info] Loading Quasi index\r\n[2016-12-13 12:44:39.836] [jointLog] [info] Loading 32-bit quasi index\r\n[2016-12-13 12:44:39.836] [stderrLog] [info] Loading Suffix Array \r\n[2016-12-13 12:44:43.439] [stderrLog] [info] Loading Transcript Info \r\n[2016-12-13 12:44:44.355] [stderrLog] [info] Loading Rank-Select Bit Array\r\n[2016-12-13 12:44:44.613] [stderrLog] [info] There were 182608 set bits in the bit array\r\n[2016-12-13 12:44:44.629] [stderrLog] [info] Computing transcript lengths\r\n[2016-12-13 12:44:44.629] [stderrLog] [info] Waiting to finish loading hash\r\n[2016-12-13 12:44:44.629] [stderrLog] [info] Done loading index\r\n[2016-12-13 12:44:44.629] [jointLog] [info] done\r\n[2016-12-13 12:44:44.629] [jointLog] [info] Index contained 182608 targets\r\n[2016-12-13 12:44:49.583] [jointLog] [warning] Fragment GC bias correction is currently *experimental* in \r\nsingle-end libraries.  Please use this option with caution.\r\n\r\n\r\n\r\nprocessed 19000000 fragments\r\nhits: 65897660; hits per frag:  3.46963\r\n\r\n\r\n\r\n[2016-12-13 12:46:51.776] [jointLog] [info] Computed 137534 rich equivalence classes for further processin\r\ng\r\n[2016-12-13 12:46:51.776] [jointLog] [info] Counted 16265961 total reads in the equivalence classes \r\n\r\n\r\n\r\n\r\n[2016-12-13 12:46:51.786] [jointLog] [info] Mapping rate = 83.509%\r\n\r\n[2016-12-13 12:46:51.786] [jointLog] [info] finished quantifyLibrary()\r\n[2016-12-13 12:46:51.786] [jointLog] [info] Starting optimizer\r\n[2016-12-13 12:46:51.867] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate\r\n[2016-12-13 12:46:51.877] [jointLog] [info] iteration = 0 | max rel diff. = 299.948\r\n[2016-12-13 12:46:51.959] [jointLog] [info] iteration 11, adjusting effective lengths to account for biase\r\ns\r\n[2016-12-13 12:52:42.161] [jointLog] [info] Computed expected counts (for bias correction)\r\n[2016-12-13 12:52:42.162] [jointLog] [info] processed bias for 0.0% of the transcripts\r\n[2016-12-13 12:53:40.240] [jointLog] [info] processed bias for 10.0% of the transcripts\r\n[2016-12-13 12:54:40.032] [jointLog] [info] processed bias for 20.0% of the transcripts\r\n[2016-12-13 12:55:40.277] [jointLog] [info] processed bias for 30.0% of the transcripts\r\n[2016-12-13 12:56:41.225] [jointLog] [info] processed bias for 40.0% of the transcripts\r\n[2016-12-13 12:57:41.888] [jointLog] [info] processed bias for 50.0% of the transcripts\r\n[2016-12-13 12:58:37.148] [jointLog] [info] processed bias for 100.0% of the transcripts\r\n[2016-12-13 12:58:37.809] [jointLog] [info] iteration = 100 | max rel diff. = 0.272558\r\n[2016-12-13 12:58:38.544] [jointLog] [info] iteration = 200 | max rel diff. = 0.213603\r\n[2016-12-13 12:58:39.275] [jointLog] [info] iteration = 300 | max rel diff. = 0.254034\r\n[2016-12-13 12:58:40.017] [jointLog] [info] iteration = 400 | max rel diff. = 0.120455\r\n[2016-12-13 12:58:40.754] [jointLog] [info] iteration = 500 | max rel diff. = 0.020828\r\n[2016-12-13 12:58:41.487] [jointLog] [info] iteration = 600 | max rel diff. = 0.0153173\r\n[2016-12-13 12:58:42.222] [jointLog] [info] iteration = 700 | max rel diff. = 0.0746574\r\n[2016-12-13 12:58:42.359] [jointLog] [info] iteration = 720 | max rel diff. = 0.00908527\r\n[2016-12-13 12:58:42.368] [jointLog] [info] Finished optimizer\r\n[2016-12-13 12:58:42.368] [jointLog] [info] writing output \r\n\r\n[2016-12-13 12:58:42.943] [jointLog] [info] Starting Gibbs Sampler\r\n  0% [>                                                    ] ETA > 1 week       \r\n```\r\n\r\nIt remained stuck at 0% until I terminated it with Control+C around 2016-12-13 14:21, nearly 1.5 hours after the Gibbs sample started. Running it again on the same sample, I see the same behavior. I'm currently re-running with different options to see if that makes a difference."},"comment":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/comments/266907058","html_url":"https://github.com/COMBINE-lab/salmon/issues/111#issuecomment-266907058","issue_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/111","id":266907058,"user":{"login":"rob-p","id":361470,"avatar_url":"https://avatars.githubusercontent.com/u/361470?v=3","gravatar_id":"","url":"https://api.github.com/users/rob-p","html_url":"https://github.com/rob-p","followers_url":"https://api.github.com/users/rob-p/followers","following_url":"https://api.github.com/users/rob-p/following{/other_user}","gists_url":"https://api.github.com/users/rob-p/gists{/gist_id}","starred_url":"https://api.github.com/users/rob-p/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rob-p/subscriptions","organizations_url":"https://api.github.com/users/rob-p/orgs","repos_url":"https://api.github.com/users/rob-p/repos","events_url":"https://api.github.com/users/rob-p/events{/privacy}","received_events_url":"https://api.github.com/users/rob-p/received_events","type":"User","site_admin":false},"created_at":"2016-12-14T00:36:34Z","updated_at":"2016-12-14T00:36:34Z","body":"Thanks!  I got the e-mail.  I'll take a look as soon as I have a chance."}}
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