{"action":"opened","issue":{"url":"https://api.github.com/repos/dereneaton/ipyrad/issues/213","repository_url":"https://api.github.com/repos/dereneaton/ipyrad","labels_url":"https://api.github.com/repos/dereneaton/ipyrad/issues/213/labels{/name}","comments_url":"https://api.github.com/repos/dereneaton/ipyrad/issues/213/comments","events_url":"https://api.github.com/repos/dereneaton/ipyrad/issues/213/events","html_url":"https://github.com/dereneaton/ipyrad/issues/213","id":197625856,"number":213,"title":"Step 2 not proceeding for some samples during execution of s12","user":{"login":"hawchuan","id":7489815,"avatar_url":"https://avatars.githubusercontent.com/u/7489815?v=3","gravatar_id":"","url":"https://api.github.com/users/hawchuan","html_url":"https://github.com/hawchuan","followers_url":"https://api.github.com/users/hawchuan/followers","following_url":"https://api.github.com/users/hawchuan/following{/other_user}","gists_url":"https://api.github.com/users/hawchuan/gists{/gist_id}","starred_url":"https://api.github.com/users/hawchuan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hawchuan/subscriptions","organizations_url":"https://api.github.com/users/hawchuan/orgs","repos_url":"https://api.github.com/users/hawchuan/repos","events_url":"https://api.github.com/users/hawchuan/events{/privacy}","received_events_url":"https://api.github.com/users/hawchuan/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-12-26T23:10:22Z","updated_at":"2016-12-26T23:10:22Z","closed_at":null,"body":"I noticed a strange issue when demuxplexing and trimming reads while doing steps1&2. After being given a barcode file and a params file, ipyrad didn't proceed to do step 2 for 4 of my samples. For the rest of the samples, they went well. Any clarification is much appreciate (or I could have missed something completely)! See partial -r output below (bad samples are CB1521 and CB1522). These 2 samples have 0 raw reads in s2_rawedit_stats.txt. Thank you!\r\n\r\nSummary stats of Assembly filter1\r\n------------------------------------------------\r\n          state  reads_raw  reads_passed_filter\r\nCB1509        2    7377462              7374025\r\nCB1510        2    5004668              5002351\r\nCB1511        2    8255477              8251831\r\nCB1512        2    7019067              7015793\r\nCB1513        2   10417587             10412173\r\nCB1514        2    6005896              6003174\r\nCB1515        2    6947835              6943605\r\nCB1516        2   10715262             10710898\r\nCB1517        2    4967166              4963402\r\nCB1518        2    3769250              3766402\r\nCB1519        2         59                   59\r\nCB1520        2   13243292             13237949\r\nCB1521        1    6172834                    0\r\nCB1522        1    3914964                    0\r\n..."}}
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