{"action":"closed","issue":{"url":"https://api.github.com/repos/marbl/canu/issues/1036","repository_url":"https://api.github.com/repos/marbl/canu","labels_url":"https://api.github.com/repos/marbl/canu/issues/1036/labels{/name}","comments_url":"https://api.github.com/repos/marbl/canu/issues/1036/comments","events_url":"https://api.github.com/repos/marbl/canu/issues/1036/events","html_url":"https://github.com/marbl/canu/issues/1036","id":349153360,"node_id":"MDU6SXNzdWUzNDkxNTMzNjA=","number":1036,"title":"Getting the canu test to work.","user":{"login":"laurafisch9","id":38894262,"node_id":"MDQ6VXNlcjM4ODk0MjYy","avatar_url":"https://avatars0.githubusercontent.com/u/38894262?v=4","gravatar_id":"","url":"https://api.github.com/users/laurafisch9","html_url":"https://github.com/laurafisch9","followers_url":"https://api.github.com/users/laurafisch9/followers","following_url":"https://api.github.com/users/laurafisch9/following{/other_user}","gists_url":"https://api.github.com/users/laurafisch9/gists{/gist_id}","starred_url":"https://api.github.com/users/laurafisch9/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/laurafisch9/subscriptions","organizations_url":"https://api.github.com/users/laurafisch9/orgs","repos_url":"https://api.github.com/users/laurafisch9/repos","events_url":"https://api.github.com/users/laurafisch9/events{/privacy}","received_events_url":"https://api.github.com/users/laurafisch9/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2018-08-09T14:29:52Z","updated_at":"2018-08-09T18:45:26Z","closed_at":"2018-08-09T18:45:25Z","author_association":"NONE","body":"I am trying to work with canu on my local macOS machine and on a linux server.\r\nAt both locations I tried to run the following command on the ecoli fasta test file\r\n\r\n```~/assemblers/canu-1.7.1/Darwin-amd64/bin/canu -p ecoli -d ecoli-oxford  genomeSize=4.8m  -nanopore-raw oxford.fasta```\r\n\r\nFor the linux server here is the issue\r\n\r\n```\r\n-- BEGIN CORRECTION\r\n--\r\n----------------------------------------\r\n-- Starting command on Thu Aug  9 10:28:19 2018 with 13395.891 GB free disk space\r\n\r\n    cd .\r\n    /slipstream/home/LauraF/assemblers/canu-1.7.1/gatekeeperCreate \\\r\n      -minlength 1000 \\\r\n      -o ./ecoli.gkpStore.BUILDING \\\r\n      ./ecoli.gkpStore.gkp \\\r\n    > ./ecoli.gkpStore.BUILDING.err 2>&1\r\n\r\n-- Finished on Thu Aug  9 10:28:19 2018 (lickety-split) with 13395.891 GB free disk space\r\n----------------------------------------\r\n\r\nERROR:\r\nERROR:  Failed with exit code 127.  (rc=32512)\r\nERROR:\r\n\r\nABORT:\r\nABORT: \r\nABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.\r\nABORT: Try restarting.  If that doesn't work, ask for help.\r\nABORT:\r\nABORT:   gatekeeper failed.\r\nABORT:\r\nABORT: Disk space available:  13395.891 GB\r\nABORT:\r\nABORT: Last 50 lines of the relevant log file (./ecoli.gkpStore.BUILDING.err):\r\nABORT:\r\nABORT:\r\n```\r\n\r\nFor my macbook here is the error that was returns\r\n\r\n```\r\n-- Running jobs.  First attempt out of 2.\r\n----------------------------------------\r\n-- Starting 'cormhap' concurrent execution on Thu Aug  9 10:13:39 2018 with 46.56 GB free disk space (3 processes; 1 concurrently)\r\n\r\n    cd correction/1-overlapper\r\n    ./precompute.sh 1 > ./precompute.000001.out 2>&1\r\n    ./precompute.sh 2 > ./precompute.000002.out 2>&1\r\n    ./precompute.sh 3 > ./precompute.000003.out 2>&1\r\n\r\n-- Finished on Thu Aug  9 10:13:40 2018 (1 second) with 46.429 GB free disk space\r\n----------------------------------------\r\n--\r\n-- Mhap precompute jobs failed, retry.\r\n--   job correction/1-overlapper/blocks/000001.dat FAILED.\r\n--   job correction/1-overlapper/blocks/000002.dat FAILED.\r\n--   job correction/1-overlapper/blocks/000003.dat FAILED.\r\n--\r\n--\r\n-- Running jobs.  Second attempt out of 2.\r\n----------------------------------------\r\n-- Starting 'cormhap' concurrent execution on Thu Aug  9 10:13:40 2018 with 46.429 GB free disk space (3 processes; 1 concurrently)\r\n\r\n    cd correction/1-overlapper\r\n    ./precompute.sh 1 > ./precompute.000001.out 2>&1\r\n    ./precompute.sh 2 > ./precompute.000002.out 2>&1\r\n    ./precompute.sh 3 > ./precompute.000003.out 2>&1\r\n\r\n-- Finished on Thu Aug  9 10:13:41 2018 (1 second) with 46.429 GB free disk space\r\n----------------------------------------\r\n--\r\n-- Mhap precompute jobs failed, tried 2 times, giving up.\r\n--   job correction/1-overlapper/blocks/000001.dat FAILED.\r\n--   job correction/1-overlapper/blocks/000002.dat FAILED.\r\n--   job correction/1-overlapper/blocks/000003.dat FAILED.\r\n--\r\n\r\nABORT:\r\nABORT: Canu 1.7.1\r\nABORT: Don't panic, but a mostly harmless error occurred and Canu stopped.\r\nABORT: Try restarting.  If that doesn't work, ask for help.\r\nABORT:\r\n```\r\n"}}
{"actor":{"display_login":"skoren"}}