{"action":"opened","issue":{"url":"https://api.github.com/repos/marcelm/cutadapt/issues/160","labels_url":"https://api.github.com/repos/marcelm/cutadapt/issues/160/labels{/name}","comments_url":"https://api.github.com/repos/marcelm/cutadapt/issues/160/comments","events_url":"https://api.github.com/repos/marcelm/cutadapt/issues/160/events","html_url":"https://github.com/marcelm/cutadapt/issues/160","id":119886133,"number":160,"title":"Output write error","user":{"login":"Protitor","id":16113820,"avatar_url":"https://avatars.githubusercontent.com/u/16113820?v=3","gravatar_id":"","url":"https://api.github.com/users/Protitor","html_url":"https://github.com/Protitor","followers_url":"https://api.github.com/users/Protitor/followers","following_url":"https://api.github.com/users/Protitor/following{/other_user}","gists_url":"https://api.github.com/users/Protitor/gists{/gist_id}","starred_url":"https://api.github.com/users/Protitor/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Protitor/subscriptions","organizations_url":"https://api.github.com/users/Protitor/orgs","repos_url":"https://api.github.com/users/Protitor/repos","events_url":"https://api.github.com/users/Protitor/events{/privacy}","received_events_url":"https://api.github.com/users/Protitor/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-12-02T07:46:00Z","updated_at":"2015-12-02T07:46:00Z","closed_at":null,"body":"Hej,\r\n\r\nI have rather a question than a real problem. I wonder if it is possible to redirect every read which is filtered to an extra file, along with the trimmed output files? I wanted to keep data loss at a minimum to go back and look into the filtered sequences at a later time point if I have to. But if I use something like:\r\n\r\n    cutadapt -a ADAPTER1 -A ADAPTER2 -m 20 -o out1.fastq -p out2.fastq --too-short-output tooshort.fastq input1.fastq input2.fastq\r\n\r\nI get the following Python error:\r\n'''Traceback (most recent call last):\r\n  File \"/home/jan/Programs/cutadapt-1.9/bin/cutadapt\", line 10, in <module>\r\n    cutadapt.main()\r\n  File \"/home/jan/Programs/cutadapt-1.9/cutadapt/scripts/cutadapt.py\", line 856, in main\r\n    stats = process_paired_reads(reader, modifiers, modifiers2, filters)\r\n  File \"/home/jan/Programs/cutadapt-1.9/cutadapt/scripts/cutadapt.py\", line 287, in process_paired_reads\r\n    if filter(read1, read2):\r\n  File \"/home/jan/Programs/cutadapt-1.9/cutadapt/filters.py\", line 68, in __call__\r\n    self.writer.write(read1, read2)\r\nTypeError: write() takes exactly 2 arguments (3 given)'''\r\n\r\nIf this is not possible at all, please try to implement an error message, so that the user can easily identify the problem (took me some while).\r\n\r\nThanks in advance,\r\nJan"}}