{"action":"created","issue":{"url":"https://api.github.com/repos/SciLifeLab/CAW/issues/388","repository_url":"https://api.github.com/repos/SciLifeLab/CAW","labels_url":"https://api.github.com/repos/SciLifeLab/CAW/issues/388/labels{/name}","comments_url":"https://api.github.com/repos/SciLifeLab/CAW/issues/388/comments","events_url":"https://api.github.com/repos/SciLifeLab/CAW/issues/388/events","html_url":"https://github.com/SciLifeLab/CAW/issues/388","id":239379220,"number":388,"title":"Problem with Ascat and R-version on Milou","user":{"login":"malinlarsson","id":3244773,"avatar_url":"https://avatars0.githubusercontent.com/u/3244773?v=3","gravatar_id":"","url":"https://api.github.com/users/malinlarsson","html_url":"https://github.com/malinlarsson","followers_url":"https://api.github.com/users/malinlarsson/followers","following_url":"https://api.github.com/users/malinlarsson/following{/other_user}","gists_url":"https://api.github.com/users/malinlarsson/gists{/gist_id}","starred_url":"https://api.github.com/users/malinlarsson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/malinlarsson/subscriptions","organizations_url":"https://api.github.com/users/malinlarsson/orgs","repos_url":"https://api.github.com/users/malinlarsson/repos","events_url":"https://api.github.com/users/malinlarsson/events{/privacy}","received_events_url":"https://api.github.com/users/malinlarsson/received_events","type":"User","site_admin":false},"labels":[{"id":342511915,"url":"https://api.github.com/repos/SciLifeLab/CAW/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2017-06-29T06:36:26Z","updated_at":"2017-06-29T09:19:20Z","closed_at":null,"body":"I got a new error in Ascat after downloading the latest CAW (I downloaded it 22 days ago, the latest commit in my version is afcc359 @marcelm marcelm Fix ConcatVCF on GRCh37. I hope this is enough information). \r\n\r\nThe error occurs in RunAscat.\r\n\r\nHere is the **.command.log** file in the work directory of this process: \r\n[malin@milou2 aa886ddee40bf3136ab5f67f139dea]$ more .command.log \r\n\r\nThe following have been reloaded with a version change:\r\n  1) java/sun_jdk1.7.0_25 => java/sun_jdk1.8.0_92\r\n\r\n\r\nLmod has detected the following error: Cannot load module \"R_packages/3.4.0\" because these modules are loaded:\r\n  R\r\n\r\nHere is the **.command.env** file from the same work directory:\r\n[malin@milou2 aa886ddee40bf3136ab5f67f139dea]$ more .command.env \r\nnxf_module_load(){\r\n  local mod=$1\r\n  local ver=${2:-}\r\n  local new_module=\"$mod\"; [[ $ver ]] && new_module+=\"/$ver\"\r\n\r\n  if [[ ! $(module list 2>&1 | grep -o \"$new_module\") ]]; then\r\n    old_module=$(module list 2>&1 | grep -Eo \"$mod\\/[^\\( \\n]+\" || true)\r\n    if [[ $ver && $old_module ]]; then\r\n      module switch $old_module $new_module\r\n    else\r\n      module load $new_module\r\n    fi\r\n  fi\r\n}\r\n\r\nnxf_module_load R 3.3.2\r\nnxf_module_load R_packages\r\nexport NXF_OPTS=\"-Xms1g -Xmx4g\"\r\nexport PATH=\"/proj/b2011185/nobackup/private/analysis/CAW/CAW/bin:$PATH\"\r\n\r\n\r\nSeems to be a clash between R-versions?"},"comment":{"url":"https://api.github.com/repos/SciLifeLab/CAW/issues/comments/311910933","html_url":"https://github.com/SciLifeLab/CAW/issues/388#issuecomment-311910933","issue_url":"https://api.github.com/repos/SciLifeLab/CAW/issues/388","id":311910933,"user":{"login":"MaxUlysse","id":1019628,"avatar_url":"https://avatars0.githubusercontent.com/u/1019628?v=3","gravatar_id":"","url":"https://api.github.com/users/MaxUlysse","html_url":"https://github.com/MaxUlysse","followers_url":"https://api.github.com/users/MaxUlysse/followers","following_url":"https://api.github.com/users/MaxUlysse/following{/other_user}","gists_url":"https://api.github.com/users/MaxUlysse/gists{/gist_id}","starred_url":"https://api.github.com/users/MaxUlysse/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MaxUlysse/subscriptions","organizations_url":"https://api.github.com/users/MaxUlysse/orgs","repos_url":"https://api.github.com/users/MaxUlysse/repos","events_url":"https://api.github.com/users/MaxUlysse/events{/privacy}","received_events_url":"https://api.github.com/users/MaxUlysse/received_events","type":"User","site_admin":false},"created_at":"2017-06-29T09:19:20Z","updated_at":"2017-06-29T09:19:20Z","body":"I'm looking into it, I think there is indeed a clash between 2 R modules."}}
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