{"action":"closed","issue":{"url":"https://api.github.com/repos/galaxyproject/galaxy/issues/3691","repository_url":"https://api.github.com/repos/galaxyproject/galaxy","labels_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/3691/labels{/name}","comments_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/3691/comments","events_url":"https://api.github.com/repos/galaxyproject/galaxy/issues/3691/events","html_url":"https://github.com/galaxyproject/galaxy/issues/3691","id":211260450,"number":3691,"title":"Trimmomatic errors with clip option at http://usegalaxy.org","user":{"login":"jennaj","id":8999735,"avatar_url":"https://avatars3.githubusercontent.com/u/8999735?v=3","gravatar_id":"","url":"https://api.github.com/users/jennaj","html_url":"https://github.com/jennaj","followers_url":"https://api.github.com/users/jennaj/followers","following_url":"https://api.github.com/users/jennaj/following{/other_user}","gists_url":"https://api.github.com/users/jennaj/gists{/gist_id}","starred_url":"https://api.github.com/users/jennaj/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jennaj/subscriptions","organizations_url":"https://api.github.com/users/jennaj/orgs","repos_url":"https://api.github.com/users/jennaj/repos","events_url":"https://api.github.com/users/jennaj/events{/privacy}","received_events_url":"https://api.github.com/users/jennaj/received_events","type":"User","site_admin":false},"labels":[{"id":180024669,"url":"https://api.github.com/repos/galaxyproject/galaxy/labels/kind/bug","name":"kind/bug","color":"84b6eb","default":false}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-03-02T01:18:19Z","updated_at":"2017-04-26T19:32:22Z","closed_at":"2017-04-26T19:32:22Z","body":"Tool produces error when option \"Perform initial ILLUMINACLIP step?\" set to \"yes\"\r\n\r\nUpdate?\r\n\r\nLatest version 0.36.2 (2/24/17): https://toolshed.g2.bx.psu.edu/view/pjbriggs/trimmomatic/141bba0e9a77\r\n\r\nMain version 0.32.3: Trimmomatic flexible read trimming tool for Illumina NGS data (Galaxy Version 0.32.3)\r\n\r\n**Example1**\r\n\r\n> Detailed Job Information\r\n>\r\n> Job ID\tXX (XX)\r\n> Tool ID\ttoolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3\r\n> Tool Version\t0.32.3\r\n> Job PID or DRM id\tXX.roundup\r\n> Job Tool Version\t\r\n> Job Execution and Failure Information\r\n> \r\n> Command Line\r\n> \r\n> bash /galaxy/main/shed_tools/toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/f8a9a5eaca8a/trimmomatic/trimmomatic.sh -mx8G -jar $TRIMMOMATIC_DIR/trimmomatic-0.32.jar PE -threads ${GALAXY_SLOTS:-6} -phred33 \"/galaxy-repl/main/files/XXX/XXX/dataset_19021843.dat\" \"/galaxy-repl/main/files/XXX/XXX/dataset_XXX.dat\" \"/galaxy-repl/main/files/XXX/XXX/dataset_XXX.dat\" \"/galaxy-repl/main/files/XXX/XXX/dataset_XXX.dat\" \"/galaxy-repl/main/files/XXX/XXX/dataset_XXX.dat\" \"/galaxy-repl/main/files/XXX/XXX/dataset_XXX.dat\" ILLUMINACLIP:$TRIMMOMATIC_ADAPTERS_DIR/TruSeq3-PE-2.fa:2:40:15 SLIDINGWINDOW:4:20\r\n> stderr\r\n> \r\n> Fatal error: Exit code 1 ()\r\n> Trimmomatic did not finish successfully\r\n\r\n**Example2**\r\n\r\n> Detailed Job Information\r\n> \r\n> Job ID\tXX (XX)\r\n> Tool ID\ttoolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3\r\n> Tool Version\t0.32.3\r\n> Job PID or DRM id\tXX.roundup\r\n> Job Tool Version\t\r\n> Job Execution and Failure Information\r\n> \r\n> Command Line\r\n> \r\n> bash /galaxy/main/shed_tools/toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/f8a9a5eaca8a/trimmomatic/trimmomatic.sh -mx8G -jar $TRIMMOMATIC_DIR/trimmomatic-0.32.jar PE -threads ${GALAXY_SLOTS:-6} -phred33 \"/galaxy-repl/main/files/XXX/XXX/dataset_XXX.dat\" \"/galaxy-repl/main/files/XXX/XXX/dataset_XXX.dat\" \"/galaxy-repl/main/files/XXX/XXX/dataset_XXX.dat\" \"/galaxy-repl/main/files/XXX/XXX/dataset_XXX.dat\" \"/galaxy-repl/main/files/XXX/XXX/dataset_XXX.dat\" \"/galaxy-repl/main/files/XXX/XXX/dataset_XXX.dat\" ILLUMINACLIP:$TRIMMOMATIC_ADAPTERS_DIR/TruSeq2-PE.fa:2:30:10 SLIDINGWINDOW:4:20\r\n> stderr\r\n> \r\n> Fatal error: Exit code 1 ()\r\n> Trimmomatic did not finish successfully\r\n\r\nMay be related to this issue: https://github.com/galaxyproject/galaxy/issues/2993"}}
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