{"action":"closed","issue":{"url":"https://api.github.com/repos/jorvis/GALES/issues/7","repository_url":"https://api.github.com/repos/jorvis/GALES","labels_url":"https://api.github.com/repos/jorvis/GALES/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/jorvis/GALES/issues/7/comments","events_url":"https://api.github.com/repos/jorvis/GALES/issues/7/events","html_url":"https://github.com/jorvis/GALES/issues/7","id":312259509,"number":7,"title":"job hmmscan stuck","user":{"login":"DavidStreid","id":7013804,"avatar_url":"https://avatars3.githubusercontent.com/u/7013804?v=4","gravatar_id":"","url":"https://api.github.com/users/DavidStreid","html_url":"https://github.com/DavidStreid","followers_url":"https://api.github.com/users/DavidStreid/followers","following_url":"https://api.github.com/users/DavidStreid/following{/other_user}","gists_url":"https://api.github.com/users/DavidStreid/gists{/gist_id}","starred_url":"https://api.github.com/users/DavidStreid/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/DavidStreid/subscriptions","organizations_url":"https://api.github.com/users/DavidStreid/orgs","repos_url":"https://api.github.com/users/DavidStreid/repos","events_url":"https://api.github.com/users/DavidStreid/events{/privacy}","received_events_url":"https://api.github.com/users/DavidStreid/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-04-08T01:15:03Z","updated_at":"2018-04-08T02:51:13Z","closed_at":"2018-04-08T02:51:13Z","author_association":"NONE","body":"I have been running the run_prok_pipeline program, but it stalls on the hmmscan. It's been stuck for about 40 minutes now. Is this expected behavior?\r\n\r\n[step hmmscan] start\r\n[job hmmscan] /private/tmp/docker_tmp7IvXQE$ docker \\\r\n    run \\\r\n    -i \\\r\n    --volume=/private/tmp/docker_tmp7IvXQE:/private/var/spool/cwl:rw \\\r\n    --volume=/private/var/folders/3b/4r8bn7v959n716gqklzhwj680000gn/T/tmp4iWvqY:/tmp:rw \\\r\n    --volume=/PATH/TO/dbs/coding_hmm.lib.bin.h3i:/private/var/lib/cwl/stg1969aaec-9073-4374-81ba-9a3c79d5f9b4/coding_hmm.lib.bin.h3i:ro \\\r\n    --volume=/PATH/TO/dbs/coding_hmm.lib.bin.h3m:/private/var/lib/cwl/stg1969aaec-9073-4374-81ba-9a3c79d5f9b4/coding_hmm.lib.bin.h3m:ro \\\r\n    --volume=/private/tmp/docker_tmpWgAsy8/prodigal2fasta.faa.part1:/private/var/lib/cwl/stg382e60be-8315-4278-a48f-c6c7a581145e/prodigal2fasta.faa.part1:ro \\\r\n    --volume=/PATH/TO/dbs/coding_hmm.lib.bin.h3f:/private/var/lib/cwl/stg1969aaec-9073-4374-81ba-9a3c79d5f9b4/coding_hmm.lib.bin.h3f:ro \\\r\n    --volume=/PATH/TO/dbs/coding_hmm.lib.bin.h3p:/private/var/lib/cwl/stg1969aaec-9073-4374-81ba-9a3c79d5f9b4/coding_hmm.lib.bin.h3p:ro \\\r\n    --volume=/PATH/TO/dbs/coding_hmm.lib.bin:/private/var/lib/cwl/stg1969aaec-9073-4374-81ba-9a3c79d5f9b4/coding_hmm.lib.bin:ro \\\r\n    --workdir=/private/var/spool/cwl \\\r\n    --read-only=true \\\r\n    --user=501:20 \\\r\n    --rm \\\r\n    --env=TMPDIR=/tmp \\\r\n    --env=HOME=/private/var/spool/cwl \\\r\n    jorvis/gales-gce \\\r\n    hmmscan \\\r\n    --acc \\\r\n    --cut_ga \\\r\n    --cpu \\\r\n    1 \\\r\n    -o \\\r\n    hmmscan.out \\\r\n    /private/var/lib/cwl/stg1969aaec-9073-4374-81ba-9a3c79d5f9b4/coding_hmm.lib.bin \\\r\n    /private/var/lib/cwl/stg382e60be-8315-4278-a48f-c6c7a581145e/prodigal2fasta.faa.part1"}}
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