{"action":"created","issue":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/261","repository_url":"https://api.github.com/repos/COMBINE-lab/salmon","labels_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/261/labels{/name}","comments_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/261/comments","events_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/261/events","html_url":"https://github.com/COMBINE-lab/salmon/issues/261","id":346033524,"node_id":"MDU6SXNzdWUzNDYwMzM1MjQ=","number":261,"title":"Segmentation fault (core dumped)","user":{"login":"csijcs","id":41136899,"node_id":"MDQ6VXNlcjQxMTM2ODk5","avatar_url":"https://avatars1.githubusercontent.com/u/41136899?v=4","gravatar_id":"","url":"https://api.github.com/users/csijcs","html_url":"https://github.com/csijcs","followers_url":"https://api.github.com/users/csijcs/followers","following_url":"https://api.github.com/users/csijcs/following{/other_user}","gists_url":"https://api.github.com/users/csijcs/gists{/gist_id}","starred_url":"https://api.github.com/users/csijcs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/csijcs/subscriptions","organizations_url":"https://api.github.com/users/csijcs/orgs","repos_url":"https://api.github.com/users/csijcs/repos","events_url":"https://api.github.com/users/csijcs/events{/privacy}","received_events_url":"https://api.github.com/users/csijcs/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-07-31T04:46:10Z","updated_at":"2018-07-31T11:40:25Z","closed_at":null,"author_association":"NONE","body":"This issue is related to salmon (bulk mode).\r\n\r\nWhen running salmon quant, everything seems to run normally until the very end, when there is suddenly \"Segmentation fault (core dumped)\" and then a quant file is not written.  Started with --gcBias, then tried with --seqBias, then without either and get the same error.  Have run Salmon in the past with no issues.  Have updated to the latest version but problem persists.\r\n\r\nThe version is salmon (mapping-based) v0.11.1 and was installed through bioconda.\r\nThe command being run is:\r\n\r\n```\r\nsalmon quant -i /data2/csijcs/hg38/hg38.transcriptome.index -l A \\\r\n         -1 ${dir}/${samp}/${samp}_R1_001.fastq.gz \\\r\n         -2 ${dir}/${samp}/${samp}_R2_001.fastq.gz \\\r\n         -p 16 -o ${dir}/salmon_quants/${samp}\r\n```\r\n\r\nThe output is:\r\n```\r\nProcessing sample PBMC_AML_BM_001\r\nVersion Info: This is the most recent version of Salmon.\r\n### salmon (mapping-based) v0.11.1\r\n### [ program ] => salmon \r\n### [ command ] => quant \r\n### [ index ] => { /data2/csijcs/hg38/hg38.transcriptome.index }\r\n### [ libType ] => { A }\r\n### [ mates1 ] => { /data2/csijcs/AML/RNA_seq/AML_total_MNC/total_MNCs/Fresh_samples/PBMC_AML_BM_001/PBMC_AML_BM_001_R1_001.fastq.gz }\r\n### [ mates2 ] => { /data2/csijcs/AML/RNA_seq/AML_total_MNC/total_MNCs/Fresh_samples/PBMC_AML_BM_001/PBMC_AML_BM_001_R2_001.fastq.gz }\r\n### [ threads ] => { 16 }\r\n### [ output ] => { /data2/csijcs/AML/RNA_seq/AML_total_MNC/total_MNCs/Fresh_samples/salmon_quants/PBMC_AML_BM_001 }\r\nLogs will be written to /data2/csijcs/AML/RNA_seq/AML_total_MNC/total_MNCs/Fresh_samples/salmon_quants/PBMC_AML_BM_001/logs\r\n[2018-07-30 15:41:42.232] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.\r\n[2018-07-30 15:41:42.232] [jointLog] [info] parsing read library format\r\n[2018-07-30 15:41:42.232] [jointLog] [info] There is 1 library.\r\n[2018-07-30 15:41:45.840] [jointLog] [info] Loading Quasi index\r\n[2018-07-30 15:41:45.840] [jointLog] [info] Loading 32-bit quasi index\r\n[2018-07-30 15:41:45.840] [stderrLog] [info] Loading Suffix Array \r\n[2018-07-30 15:42:39.168] [stderrLog] [info] Loading Transcript Info \r\n[2018-07-30 15:42:53.599] [stderrLog] [info] Loading Rank-Select Bit Array\r\n[2018-07-30 15:42:56.236] [stderrLog] [info] There were 203027 set bits in the bit array\r\n[2018-07-30 15:42:56.328] [stderrLog] [info] Computing transcript lengths\r\n[2018-07-30 15:42:56.329] [stderrLog] [info] Waiting to finish loading hash\r\n[2018-07-30 15:42:56.329] [stderrLog] [info] Done loading index\r\n[2018-07-30 15:42:56.329] [jointLog] [info] done\r\n[2018-07-30 15:42:56.329] [jointLog] [info] Index contained 203027 targets\r\n\r\nprocessed 4000003 fragments\r\nprocessed 298000000 fragments 0.071773[2018-07-30 15:43:47.415] [jointLog] [info] Automatically detected most likely library type as IU\r\nhits: 20950511, hits per frag:  0.0703073[2018-07-30 16:26:22.399] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments\r\n[2018-07-30 16:26:22.399] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments\r\n[2018-07-30 16:26:22.399] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments\r\n[2018-07-30 16:26:22.432] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments\r\n[2018-07-30 16:26:22.469] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments\r\n[2018-07-30 16:26:22.513] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments\r\n[2018-07-30 16:26:22.582] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments\r\n[2018-07-30 16:26:22.605] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments\r\n[2018-07-30 16:26:22.631] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments\r\n[2018-07-30 16:26:22.678] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments\r\n[2018-07-30 16:26:22.679] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments\r\n[2018-07-30 16:26:22.739] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments\r\n[2018-07-30 16:26:22.771] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments\r\n[2018-07-30 16:26:22.807] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments\r\n[2018-07-30 16:26:22.828] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments\r\n[2018-07-30 16:26:22.896] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments\r\n\r\nSegmentation fault (core dumped)\r\n```\r\n\r\nThe environment is Linux Elmo 3.16.0-77-generic #99~14.04.1-Ubuntu SMP Tue Jun 28 19:17:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux\r\n\r\nAny help would be much appreciated"},"comment":{"url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/comments/409190463","html_url":"https://github.com/COMBINE-lab/salmon/issues/261#issuecomment-409190463","issue_url":"https://api.github.com/repos/COMBINE-lab/salmon/issues/261","id":409190463,"node_id":"MDEyOklzc3VlQ29tbWVudDQwOTE5MDQ2Mw==","user":{"login":"rob-p","id":361470,"node_id":"MDQ6VXNlcjM2MTQ3MA==","avatar_url":"https://avatars3.githubusercontent.com/u/361470?v=4","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":"2018-07-31T11:40:24Z","updated_at":"2018-07-31T11:40:24Z","author_association":"CONTRIBUTOR","body":"Hi @csijcs,\r\n\r\n  Obviously, a segfault should not be happening, regardless of the input.  However, one thing that stands out here is that the mapping rate looks super low ... about 0.07 hits per fragment, with up to 0.06 of them being discarded as 0 probability.  Can you share the first few million reads, and let me know the exact transcriptome you indexed.  I can try and see whats going on.  Is there anything obviously wonky with the reads?\r\n\r\nBest,\r\nRob"}}
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