{"action":"opened","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/813","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/813/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/813/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/813/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/813","id":66813800,"number":813,"title":"Pipeline passes wrong chanjo arguments","user":{"login":"LMannarino","id":11782567,"avatar_url":"https://avatars.githubusercontent.com/u/11782567?v=3","gravatar_id":"","url":"https://api.github.com/users/LMannarino","html_url":"https://github.com/LMannarino","followers_url":"https://api.github.com/users/LMannarino/followers","following_url":"https://api.github.com/users/LMannarino/following{/other_user}","gists_url":"https://api.github.com/users/LMannarino/gists{/gist_id}","starred_url":"https://api.github.com/users/LMannarino/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/LMannarino/subscriptions","organizations_url":"https://api.github.com/users/LMannarino/orgs","repos_url":"https://api.github.com/users/LMannarino/repos","events_url":"https://api.github.com/users/LMannarino/events{/privacy}","received_events_url":"https://api.github.com/users/LMannarino/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-04-07T07:59:22Z","updated_at":"2015-04-07T07:59:22Z","closed_at":null,"body":"(CC @lbeltrame)\r\n\r\nWhen running chanjo, it looks like the program arguments are not being sent correctly. Here is the log (single-core run):\r\n\r\n````\r\nsubprocess.CalledProcessError: Command 'set -o pipefail; /mnt/data/bcbio/anaconda/bin/chanjo annotate -s 21184-blood -g  -c 4 /mnt/data/projects/OV198/OV198/work/align/21184-blood/90_2015-04-02_OV198-sort.bam /mnt/data/projects/OV198/OV198/work/coverage/panelAB.sorted-unames.bed | /mnt/data/bcbio/anaconda/bin/chanjo --db /mnt/data/projects/OV198/OV198/work/coverage/tx/tmpvcoQLR/-coverage.db import\r\nUsage: chanjo annotate [OPTIONS] BAM_PATH [IN_STREAM]\r\n\r\nError: Invalid value for \"bam_path\": Path \"4\" does not exist.\r\n````\r\n\r\nI last updated the pipeline last Friday (Apr 3th 2015)."}}