{"action":"created","issue":{"url":"https://api.github.com/repos/benedictpaten/marginAlign/issues/21","repository_url":"https://api.github.com/repos/benedictpaten/marginAlign","labels_url":"https://api.github.com/repos/benedictpaten/marginAlign/issues/21/labels{/name}","comments_url":"https://api.github.com/repos/benedictpaten/marginAlign/issues/21/comments","events_url":"https://api.github.com/repos/benedictpaten/marginAlign/issues/21/events","html_url":"https://github.com/benedictpaten/marginAlign/issues/21","id":121915294,"number":21,"title":"marginCaller - no such file 'posteriorProbs.txt'","user":{"login":"demharters","id":3235790,"avatar_url":"https://avatars.githubusercontent.com/u/3235790?v=3","gravatar_id":"","url":"https://api.github.com/users/demharters","html_url":"https://github.com/demharters","followers_url":"https://api.github.com/users/demharters/followers","following_url":"https://api.github.com/users/demharters/following{/other_user}","gists_url":"https://api.github.com/users/demharters/gists{/gist_id}","starred_url":"https://api.github.com/users/demharters/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/demharters/subscriptions","organizations_url":"https://api.github.com/users/demharters/orgs","repos_url":"https://api.github.com/users/demharters/repos","events_url":"https://api.github.com/users/demharters/events{/privacy}","received_events_url":"https://api.github.com/users/demharters/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":{"login":"mitenjain","id":2062794,"avatar_url":"https://avatars.githubusercontent.com/u/2062794?v=3","gravatar_id":"","url":"https://api.github.com/users/mitenjain","html_url":"https://github.com/mitenjain","followers_url":"https://api.github.com/users/mitenjain/followers","following_url":"https://api.github.com/users/mitenjain/following{/other_user}","gists_url":"https://api.github.com/users/mitenjain/gists{/gist_id}","starred_url":"https://api.github.com/users/mitenjain/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mitenjain/subscriptions","organizations_url":"https://api.github.com/users/mitenjain/orgs","repos_url":"https://api.github.com/users/mitenjain/repos","events_url":"https://api.github.com/users/mitenjain/events{/privacy}","received_events_url":"https://api.github.com/users/mitenjain/received_events","type":"User","site_admin":false},"milestone":null,"comments":1,"created_at":"2015-12-13T11:56:39Z","updated_at":"2016-02-25T20:42:16Z","closed_at":"2016-02-25T20:42:16Z","body":"When trying to call SNVs with marginCaller the programme crashes and I get the following output (I am only posting one instance of many identical messages):\r\n\r\n**Mac OS X (El Capitan):**\r\n$ marginCaller input.sam reference.fasta output.vcf\r\n/Users/sam/software/marginAlign/src/margin/mappers/last_hmm_20.txt\r\n0.3\r\nThe job seems to have left a log file, indicating failure: /Users/sam/jobTree/jobs/t3/t2/job\r\nReporting file: /Users/sam/jobTree/jobs/t3/t2/log.txt\r\nlog.txt:\t---JOBTREE SLAVE OUTPUT LOG---\r\nlog.txt:\t/bin/sh: 939732440: command not found\r\nlog.txt:\t/bin/sh: gb: command not found\r\nlog.txt:\t/bin/sh: CP011343.2: command not found\r\nlog.txt:\t/bin/sh: 2403236: command not found\r\nlog.txt:\tTraceback (most recent call last):\r\nlog.txt:\t  File \"/Users/sam/software/marginAlign/submodules/jobTree/src/jobTreeSlave.py\", line 271, in main\r\nlog.txt:\t    defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)\r\nlog.txt:\t  File \"/Users/sam/software/marginAlign/submodules/jobTree/scriptTree/stack.py\", line 153, in execute\r\nlog.txt:\t    self.target.run()\r\nlog.txt:\t  File \"/Users/sam/software/marginAlign/submodules/jobTree/scriptTree/target.py\", line 197, in run\r\nlog.txt:\t    func(*((self,) + tuple(self.args)), **self.kwargs)\r\nlog.txt:\t  File \"/Users/sam/software/marginAlign/src/margin/marginCallerLib.py\", line 61, in posteriorProbabilityCalculationTargetFn\r\nlog.txt:\t    map(lambda x : map(float, x.split()), open(tempPosteriorProbsFile, 'r')):\r\nlog.txt:\tIOError: [Errno 2] No such file or directory: '/var/folders/lr/ws3f8_kd2p343vqcrj36w7z40000gn/T/tmpomTYBS/localTempDir/posteriorProbs.txt'\r\nlog.txt:\tExiting the slave because of a failed job on host Macbook\r\nlog.txt:\tDue to failure we are reducing the remaining retry count of job /Users/sam/jobTree/jobs/t3/t2/job to 0\r\nlog.txt:\tWe have set the default memory of the failed job to 2147483648 bytes\r\nJob: /Users/sam/jobTree/jobs/t3/t2/job is completely failed\r\n\r\n**Linux (Red Hat Enterprise Linux Server release 6.3 (Santiago)):**\r\n$ marginCaller output.sam referenceBC01.fasta output.vcf\r\n/home/coml-nmsi/sdemharter/software/marginAlign/src/margin/mappers/last_hmm_20.txt\r\n0.3\r\nThe job seems to have left a log file, indicating failure: /data/coml-nmsi/sdemharter/ont/jobTree/jobs/t0/t0/t1/job\r\nReporting file: /data/coml-nmsi/sdemharter/ont/jobTree/jobs/t0/t0/t1/log.txt\r\nlog.txt:        ---JOBTREE SLAVE OUTPUT LOG---\r\nlog.txt:        /bin/sh: gb: command not found\r\nlog.txt:        /bin/sh: 173474: command not found\r\nlog.txt:        /bin/sh: CP011343.2: command not found\r\nlog.txt:        /bin/sh: 939732440: command not found\r\nlog.txt:        Traceback (most recent call last):\r\nlog.txt:          File \"/home/coml-nmsi/sdemharter/software/marginAlign/submodules/jobTree/src/jobTreeSlave.py\", line 271, in main\r\nlog.txt:            defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)\r\nlog.txt:          File \"/home/coml-nmsi/sdemharter/software/marginAlign/submodules/jobTree/scriptTree/stack.py\", line 153, in execute\r\nlog.txt:            self.target.run()\r\nlog.txt:          File \"/home/coml-nmsi/sdemharter/software/marginAlign/submodules/jobTree/scriptTree/target.py\", line 197, in run\r\nlog.txt:            func(*((self,) + tuple(self.args)), **self.kwargs)\r\nlog.txt:          File \"/home/coml-nmsi/sdemharter/software/marginAlign/src/margin/marginCallerLib.py\", line 62, in posteriorProbabilityCalculationTargetFn\r\nlog.txt:            map(lambda x : map(float, x.split()), open(tempPosteriorProbsFile, 'r')):\r\nlog.txt:        IOError: [Errno 2] No such file or directory: '/tmp/tmpX__aXV/localTempDir/posteriorProbs.txt'\r\nlog.txt:        Exiting the slave because of a failed job on host login3\r\nlog.txt:        Due to failure we are reducing the remaining retry count of job /data/coml-nmsi/sdemharter/ont/jobTree/jobs/t0/t0/t1/job to 0\r\nlog.txt:        We have set the default memory of the failed job to 2147483648 bytes\r\nJob: /data/coml-nmsi/sdemharter/ont/jobTree/jobs/t0/t0/t1/job is completely failed"},"comment":{"url":"https://api.github.com/repos/benedictpaten/marginAlign/issues/comments/188975068","html_url":"https://github.com/benedictpaten/marginAlign/issues/21#issuecomment-188975068","issue_url":"https://api.github.com/repos/benedictpaten/marginAlign/issues/21","id":188975068,"user":{"login":"mitenjain","id":2062794,"avatar_url":"https://avatars.githubusercontent.com/u/2062794?v=3","gravatar_id":"","url":"https://api.github.com/users/mitenjain","html_url":"https://github.com/mitenjain","followers_url":"https://api.github.com/users/mitenjain/followers","following_url":"https://api.github.com/users/mitenjain/following{/other_user}","gists_url":"https://api.github.com/users/mitenjain/gists{/gist_id}","starred_url":"https://api.github.com/users/mitenjain/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mitenjain/subscriptions","organizations_url":"https://api.github.com/users/mitenjain/orgs","repos_url":"https://api.github.com/users/mitenjain/repos","events_url":"https://api.github.com/users/mitenjain/events{/privacy}","received_events_url":"https://api.github.com/users/mitenjain/received_events","type":"User","site_admin":false},"created_at":"2016-02-25T20:42:16Z","updated_at":"2016-02-25T20:42:16Z","body":"The marginCaller module was crashing due to special characters in fasta file. I am fixing it on a branch, and will update this."}}