{"action":"created","issue":{"url":"https://api.github.com/repos/biosails/pheniqs/issues/16","repository_url":"https://api.github.com/repos/biosails/pheniqs","labels_url":"https://api.github.com/repos/biosails/pheniqs/issues/16/labels{/name}","comments_url":"https://api.github.com/repos/biosails/pheniqs/issues/16/comments","events_url":"https://api.github.com/repos/biosails/pheniqs/issues/16/events","html_url":"https://github.com/biosails/pheniqs/issues/16","id":369635767,"node_id":"MDU6SXNzdWUzNjk2MzU3Njc=","number":16,"title":"Pheniqs only processes a small fraction of reads","user":{"login":"rspreafico-sgi","id":34698433,"node_id":"MDQ6VXNlcjM0Njk4NDMz","avatar_url":"https://avatars2.githubusercontent.com/u/34698433?v=4","gravatar_id":"","url":"https://api.github.com/users/rspreafico-sgi","html_url":"https://github.com/rspreafico-sgi","followers_url":"https://api.github.com/users/rspreafico-sgi/followers","following_url":"https://api.github.com/users/rspreafico-sgi/following{/other_user}","gists_url":"https://api.github.com/users/rspreafico-sgi/gists{/gist_id}","starred_url":"https://api.github.com/users/rspreafico-sgi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rspreafico-sgi/subscriptions","organizations_url":"https://api.github.com/users/rspreafico-sgi/orgs","repos_url":"https://api.github.com/users/rspreafico-sgi/repos","events_url":"https://api.github.com/users/rspreafico-sgi/events{/privacy}","received_events_url":"https://api.github.com/users/rspreafico-sgi/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":13,"created_at":"2018-10-12T17:09:15Z","updated_at":"2018-11-09T01:42:20Z","closed_at":null,"author_association":"NONE","body":"Hi, I am trying trying to demux a PE run using inline barcodes on read 2:\r\n\r\n```\r\n{\r\n    \"input\": [\r\n        \"LS01-2018-09-24-LS-UA-CAAF-001_R1_001.fastq.gz\",\r\n        \"LS01-2018-09-24-LS-UA-CAAF-001_R2_001.fastq.gz\"\r\n    ],\r\n    \"transform\": { \r\n        \"token\": [ \"0::\", \"1:14:\" ],\r\n        \"segment pattern\": [ \"0\", \"1\" ]\r\n    },\r\n    \"multiplex\": {\r\n        \"transform\": { \"token\": [ \"1::12\" ] },\r\n        \"codec\": {\r\n            \"@TATGAACGTCCG\": { \"barcode\": [ \"TATGAACGTCCG\" ], \"output\": [ \"BC4CAAF1-10m-20180912-1120_L001_R1_001.fastq.gz\", \"BC4CAAF1-10m-20180912-1120_L001_R2_001.fastq.gz\" ] },\r\n            \"@CCACATTGGGTC\": { \"barcode\": [ \"CCACATTGGGTC\" ], \"output\": [ \"BC1CAAF1-200m-20180912-0920_L001_R1_001.fastq.gz\", \"BC1CAAF1-200m-20180912-0920_L001_R2_001.fastq.gz\" ] },\r\n            \"@TCAGTCAGATGA\": { \"barcode\": [ \"TCAGTCAGATGA\" ], \"output\": [ \"BC4CAAF1-10m-20180912-1015_L001_R1_001.fastq.gz\", \"BC4CAAF1-10m-20180912-1015_L001_R2_001.fastq.gz\" ] },\r\n            \"@AAGTCACACACA\": { \"barcode\": [ \"AAGTCACACACA\" ], \"output\": [ \"BC1CAAF1-200m-20180912-1020_L001_R1_001.fastq.gz\", \"BC1CAAF1-200m-20180912-1020_L001_R2_001.fastq.gz\" ] },\r\n            \"@GCTGTGATTCGA\": { \"barcode\": [ \"GCTGTGATTCGA\" ], \"output\": [ \"BC2CAAF2-200m-20180912-0920_L001_R1_001.fastq.gz\", \"BC2CAAF2-200m-20180912-0920_L001_R2_001.fastq.gz\" ] }\r\n        },\r\n        \"undetermined\": { \"output\": [ \"LS01-undetermined_L001_R1_001.fastq.gz\", \"LS01-undetermined_L001_R2_001.fastq.gz\" ] },\r\n        \"algorithm\": \"mdd\",\r\n        \"include filtered\": true\r\n    }\r\n}\r\n```\r\n\r\nHowever, I always get back only 116 reads, despite the fact that the two input files have thousands of reads. I have tried with PAML too, same results.\r\n\r\n```\r\n{\r\n    \"multiplex\": {\r\n        \"average classified distance\": 0.219298245614035,\r\n        \"average pf classified distance\": 0.219298245614035,\r\n        \"classified\": [\r\n            {\r\n                \"ID\": \"AAGTCACACACA\",\r\n                \"PU\": \"AAGTCACACACA\",\r\n                \"average distance\": 0.461538461538461,\r\n                \"average pf distance\": 0.461538461538461,\r\n                \"barcode\": [\r\n                    \"AAGTCACACACA\"\r\n                ],\r\n                \"concentration\": 0.198,\r\n                \"count\": 13,\r\n                \"index\": 1,\r\n                \"pf count\": 13,\r\n                \"pf fraction\": 1.0,\r\n                \"pf pooled classified fraction\": 0.114035087719298,\r\n                \"pf pooled fraction\": 0.112068965517241,\r\n                \"pooled classified fraction\": 0.114035087719298,\r\n                \"pooled fraction\": 0.112068965517241\r\n            },\r\n            {\r\n                \"ID\": \"CCACATTGGGTC\",\r\n                \"PU\": \"CCACATTGGGTC\",\r\n                \"average distance\": 0.071428571428571,\r\n                \"average pf distance\": 0.071428571428571,\r\n                \"barcode\": [\r\n                    \"CCACATTGGGTC\"\r\n                ],\r\n                \"concentration\": 0.198,\r\n                \"count\": 28,\r\n                \"index\": 2,\r\n                \"pf count\": 28,\r\n                \"pf fraction\": 1.0,\r\n                \"pf pooled classified fraction\": 0.245614035087719,\r\n                \"pf pooled fraction\": 0.241379310344827,\r\n                \"pooled classified fraction\": 0.245614035087719,\r\n                \"pooled fraction\": 0.241379310344827\r\n            },\r\n            {\r\n                \"ID\": \"GCTGTGATTCGA\",\r\n                \"PU\": \"GCTGTGATTCGA\",\r\n                \"average distance\": 0.260869565217391,\r\n                \"average pf distance\": 0.260869565217391,\r\n                \"barcode\": [\r\n                    \"GCTGTGATTCGA\"\r\n                ],\r\n                \"concentration\": 0.198,\r\n                \"count\": 46,\r\n                \"index\": 3,\r\n                \"pf count\": 46,\r\n                \"pf fraction\": 1.0,\r\n                \"pf pooled classified fraction\": 0.403508771929824,\r\n                \"pf pooled fraction\": 0.396551724137931,\r\n                \"pooled classified fraction\": 0.403508771929824,\r\n                \"pooled fraction\": 0.396551724137931\r\n            },\r\n            {\r\n                \"ID\": \"TATGAACGTCCG\",\r\n                \"PU\": \"TATGAACGTCCG\",\r\n                \"average distance\": 1.0,\r\n                \"average pf distance\": 1.0,\r\n                \"barcode\": [\r\n                    \"TATGAACGTCCG\"\r\n                ],\r\n                \"concentration\": 0.198,\r\n                \"count\": 1,\r\n                \"index\": 4,\r\n                \"pf count\": 1,\r\n                \"pf fraction\": 1.0,\r\n                \"pf pooled classified fraction\": 0.008771929824561,\r\n                \"pf pooled fraction\": 0.008620689655172,\r\n                \"pooled classified fraction\": 0.008771929824561,\r\n                \"pooled fraction\": 0.008620689655172\r\n            },\r\n            {\r\n                \"ID\": \"TCAGTCAGATGA\",\r\n                \"PU\": \"TCAGTCAGATGA\",\r\n                \"average distance\": 0.153846153846153,\r\n                \"average pf distance\": 0.153846153846153,\r\n                \"barcode\": [\r\n                    \"TCAGTCAGATGA\"\r\n                ],\r\n                \"concentration\": 0.198,\r\n                \"count\": 26,\r\n                \"index\": 5,\r\n                \"pf count\": 26,\r\n                \"pf fraction\": 1.0,\r\n                \"pf pooled classified fraction\": 0.228070175438596,\r\n                \"pf pooled fraction\": 0.224137931034482,\r\n                \"pooled classified fraction\": 0.228070175438596,\r\n                \"pooled fraction\": 0.224137931034482\r\n            }\r\n        ],\r\n        \"classified count\": 114,\r\n        \"classified fraction\": 0.982758620689655,\r\n        \"classified pf fraction\": 1.0,\r\n        \"count\": 116,\r\n        \"pf classified count\": 114,\r\n        \"pf classified fraction\": 0.982758620689655,\r\n        \"pf count\": 116,\r\n        \"pf fraction\": 1.0,\r\n        \"unclassified\": {\r\n            \"ID\": \"undetermined\",\r\n            \"PU\": \"undetermined\",\r\n            \"count\": 2,\r\n            \"index\": 0,\r\n            \"pf count\": 2,\r\n            \"pf fraction\": 1.0,\r\n            \"pf pooled classified fraction\": 0.017543859649122,\r\n            \"pf pooled fraction\": 0.017241379310344,\r\n            \"pooled classified fraction\": 0.017543859649122,\r\n            \"pooled fraction\": 0.017241379310344\r\n        }\r\n    }\r\n}\r\n```"},"comment":{"url":"https://api.github.com/repos/biosails/pheniqs/issues/comments/437220402","html_url":"https://github.com/biosails/pheniqs/issues/16#issuecomment-437220402","issue_url":"https://api.github.com/repos/biosails/pheniqs/issues/16","id":437220402,"node_id":"MDEyOklzc3VlQ29tbWVudDQzNzIyMDQwMg==","user":{"login":"rspreafico-sgi","id":34698433,"node_id":"MDQ6VXNlcjM0Njk4NDMz","avatar_url":"https://avatars2.githubusercontent.com/u/34698433?v=4","gravatar_id":"","url":"https://api.github.com/users/rspreafico-sgi","html_url":"https://github.com/rspreafico-sgi","followers_url":"https://api.github.com/users/rspreafico-sgi/followers","following_url":"https://api.github.com/users/rspreafico-sgi/following{/other_user}","gists_url":"https://api.github.com/users/rspreafico-sgi/gists{/gist_id}","starred_url":"https://api.github.com/users/rspreafico-sgi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rspreafico-sgi/subscriptions","organizations_url":"https://api.github.com/users/rspreafico-sgi/orgs","repos_url":"https://api.github.com/users/rspreafico-sgi/repos","events_url":"https://api.github.com/users/rspreafico-sgi/events{/privacy}","received_events_url":"https://api.github.com/users/rspreafico-sgi/received_events","type":"User","site_admin":false},"created_at":"2018-11-09T01:42:20Z","updated_at":"2018-11-09T01:42:20Z","author_association":"NONE","body":"Decompressing the same with gunzip works fine"}}
{"actor":{"display_login":"rspreafico-sgi"}}