If I run this as follows there are no problems
$ /Git/progressiveCactus/bin/runProgressiveCactus.sh --overwrite seq2 ./work2/ seq2.hal
However, I want to specify r1 as the root, and avoid getting the "anc0" sequence added to the alignment.
When I specify the root it crashes
$ /Git/progressiveCactus/bin/runProgressiveCactus.sh --overwrite --root=r1 --logDebug --logFile=seq2.log seq2 ./work2/ seq2.hal
Logging set at level: DEBUG
Logging to file: seq2.log
No branch length for r1: setting to 1
No branch length for r2: setting to 1
No branch length for r2i: setting to 1
No branch length for : setting to 1
No branch length for : setting to 1
Running the command: cactus_analyseAssembly r1.fa
Running the command: cactus_analyseAssembly r2.fa
Running the command: cactus_analyseAssembly r2i.fa
The job seems to have left a log file, indicating failure: /align/work2/jobTree/jobs/job
Reporting file: /align/work2/jobTree/jobs/log.txt
log.txt: ---JOBTREE SLAVE OUTPUT LOG---
log.txt: Traceback (most recent call last):
log.txt: File "/Git/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main
log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth)
log.txt: File "/Git/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute
log.txt: self.target.run()
log.txt: File "/Git/progressiveCactus/submodules/cactus/progressive/cactus_progressive.py", line 193, in run
log.txt: configNode = ET.parse(project.getConfigPath()).getroot()
log.txt: File "/Git/progressiveCactus/submodules/cactus/progressive/multiCactusProject.py", line 105, in getConfigPath
log.txt: return ExperimentWrapper(ET.parse(self.expMap.values()[0]).getroot()).getConfigPath()
log.txt: IndexError: list index out of range
log.txt: Exiting the slave because of a failed job on host rs-bt-cb-moira
log.txt: Due to failure we are reducing the remaining retry count of job /align/work2/jobTree/jobs/job to 0
log.txt: We have set the default memory of the failed job to 2147483648.0 bytes
Job: /align/work2/jobTree/jobs/job is completely failed
I am trying to run progressiveCactus on 3 sequences, arranged as follows:
$ cat seq2 (r1,(r2,(r2i))); *r1 r1..fa r2 r2.fa r2i r2i.fa
If I run this as follows there are no problems $ /Git/progressiveCactus/bin/runProgressiveCactus.sh --overwrite seq2 ./work2/ seq2.hal
However, I want to specify r1 as the root, and avoid getting the "anc0" sequence added to the alignment.
When I specify the root it crashes $ /Git/progressiveCactus/bin/runProgressiveCactus.sh --overwrite --root=r1 --logDebug --logFile=seq2.log seq2 ./work2/ seq2.hal Logging set at level: DEBUG Logging to file: seq2.log No branch length for r1: setting to 1 No branch length for r2: setting to 1 No branch length for r2i: setting to 1 No branch length for : setting to 1 No branch length for : setting to 1 Running the command: cactus_analyseAssembly r1.fa Running the command: cactus_analyseAssembly r2.fa Running the command: cactus_analyseAssembly r2i.fa
]$ cat ./work2/cactus.log
2016-02-11 10:56:39.038343: Beginning Progressive Cactus Alignment
The job seems to have left a log file, indicating failure: /align/work2/jobTree/jobs/job Reporting file: /align/work2/jobTree/jobs/log.txt log.txt: ---JOBTREE SLAVE OUTPUT LOG--- log.txt: Traceback (most recent call last): log.txt: File "/Git/progressiveCactus/submodules/jobTree/src/jobTreeSlave.py", line 271, in main log.txt: defaultMemory=defaultMemory, defaultCpu=defaultCpu, depth=depth) log.txt: File "/Git/progressiveCactus/submodules/jobTree/scriptTree/stack.py", line 153, in execute log.txt: self.target.run() log.txt: File "/Git/progressiveCactus/submodules/cactus/progressive/cactus_progressive.py", line 193, in run log.txt: configNode = ET.parse(project.getConfigPath()).getroot() log.txt: File "/Git/progressiveCactus/submodules/cactus/progressive/multiCactusProject.py", line 105, in getConfigPath log.txt: return ExperimentWrapper(ET.parse(self.expMap.values()[0]).getroot()).getConfigPath() log.txt: IndexError: list index out of range log.txt: Exiting the slave because of a failed job on host rs-bt-cb-moira log.txt: Due to failure we are reducing the remaining retry count of job /align/work2/jobTree/jobs/job to 0 log.txt: We have set the default memory of the failed job to 2147483648.0 bytes Job: /align/work2/jobTree/jobs/job is completely failed
2016-02-11 10:56:39.454932: Finished Progressive Cactus Alignment
Any suggestions on how to fix this? Thanks, Juan