marginCaller - no such file 'posteriorProbs.txt'

[demharters]

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):

Mac OS X (El Capitan): $ marginCaller input.sam reference.fasta output.vcf /Users/sam/software/marginAlign/src/margin/mappers/last_hmm20.txt 0.3 The job seems to have left a log file, indicating failure: /Users/sam/jobTree/jobs/t3/t2/job Reporting file: /Users/sam/jobTree/jobs/t3/t2/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: /bin/sh: 939732440: command not found log.txt: /bin/sh: gb: command not found log.txt: /bin/sh: CP011343.2: command not found log.txt: /bin/sh: 2403236: command not found log.txt: Traceback (most recent call last): log.txt: File "/Users/sam/software/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/Users/sam/software/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/Users/sam/software/marginAlign/submodules/jobTree/scriptTree/target.py", line 197, in run log.txt: func(((self,) + tuple(self.args)), *_self.kwargs) log.txt: File "/Users/sam/software/marginAlign/src/margin/marginCallerLib.py", line 61, in posteriorProbabilityCalculationTargetFn log.txt: map(lambda x : map(float, x.split()), open(tempPosteriorProbsFile, 'r')): log.txt: IOError: [Errno 2] No such file or directory: '/var/folders/lr/ws3f8_kd2p343vqcrj36w7z40000gn/T/tmpomTYBS/localTempDir/posteriorProbs.txt' log.txt: Exiting the slave because of a failed job on host Macbook log.txt: Due to failure we are reducing the remaining retry count of job /Users/sam/jobTree/jobs/t3/t2/job to 0 log.txt: We have set the default memory of the failed job to 2147483648 bytes Job: /Users/sam/jobTree/jobs/t3/t2/job is completely failed

Linux (Red Hat Enterprise Linux Server release 6.3 (Santiago)): $ marginCaller output.sam referenceBC01.fasta output.vcf /home/coml-nmsi/sdemharter/software/marginAlign/src/margin/mappers/last_hmm20.txt 0.3 The job seems to have left a log file, indicating failure: /data/coml-nmsi/sdemharter/ont/jobTree/jobs/t0/t0/t1/job Reporting file: /data/coml-nmsi/sdemharter/ont/jobTree/jobs/t0/t0/t1/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: /bin/sh: gb: command not found log.txt: /bin/sh: 173474: command not found log.txt: /bin/sh: CP011343.2: command not found log.txt: /bin/sh: 939732440: command not found log.txt: Traceback (most recent call last): log.txt: File "/home/coml-nmsi/sdemharter/software/marginAlign/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/home/coml-nmsi/sdemharter/software/marginAlign/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/home/coml-nmsi/sdemharter/software/marginAlign/submodules/jobTree/scriptTree/target.py", line 197, in run log.txt: func(((self,) + tuple(self.args)), *_self.kwargs) log.txt: File "/home/coml-nmsi/sdemharter/software/marginAlign/src/margin/marginCallerLib.py", line 62, in posteriorProbabilityCalculationTargetFn log.txt: map(lambda x : map(float, x.split()), open(tempPosteriorProbsFile, 'r')): log.txt: IOError: [Errno 2] No such file or directory: '/tmp/tmpX__aXV/localTempDir/posteriorProbs.txt' log.txt: Exiting the slave because of a failed job on host login3 log.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 log.txt: We have set the default memory of the failed job to 2147483648 bytes Job: /data/coml-nmsi/sdemharter/ont/jobTree/jobs/t0/t0/t1/job is completely failed

[mitenjain]

The marginCaller module was crashing due to special characters in fasta file. I am fixing it on a branch, and will update this.

[mitenjain]

Need to fix ASAP

[mitenjain]

This should be fixed now.