Hi,
I am currently struggling to get progressiveCactus to run. Since the progressiveCactus github is not very responsive, I hope to get some input here.
I managed to install progressiveCactus on my torque/pbs cluster, after manually installing argparse and importlib modules with easy_install. When I then try to run the example with
it starts nicely.
However, the program does not progress in any way and I don’t see any related processes running. The log file only says: Beginning the alignment. I reran the example in debug mode and here’s what the logfile contained:
In addition, I see some idle processes running, which are likely started by progressiveCactus.
Does anyone have an idea what is causing this behaviour and whether there is any chance I can get progressiveCactus running on this system?
- lukas
I am currently struggling to get progressiveCactus to run. Since the progressiveCactus github is not very responsive, I hope to get some input here.
I managed to install progressiveCactus on my torque/pbs cluster, after manually installing argparse and importlib modules with easy_install. When I then try to run the example with
Code:
(bin/runProgressiveCactus.sh examples/blanchette00.txt ./work ./work/b00.hal)
However, the program does not progress in any way and I don’t see any related processes running. The log file only says: Beginning the alignment. I reran the example in debug mode and here’s what the logfile contained:
Code:
Logging to file: cac1.log Running the command: cactus_analyseAssembly ./submodules/cactusTestData/blanchettesSimulation/00.job/HUMAN Running the command: cactus_analyseAssembly ./submodules/cactusTestData/blanchettesSimulation/00.job/CHIMP Running the command: cactus_analyseAssembly ./submodules/cactusTestData/blanchettesSimulation/00.job/BABOON Running the command: cactus_analyseAssembly ./submodules/cactusTestData/blanchettesSimulation/00.job/MOUSE Running the command: cactus_analyseAssembly ./submodules/cactusTestData/blanchettesSimulation/00.job/RAT Running the command: cactus_analyseAssembly ./submodules/cactusTestData/blanchettesSimulation/00.job/DOG Running the command: cactus_analyseAssembly ./submodules/cactusTestData/blanchettesSimulation/00.job/CAT Running the command: cactus_analyseAssembly ./submodules/cactusTestData/blanchettesSimulation/00.job/PIG Running the command: cactus_analyseAssembly ./submodules/cactusTestData/blanchettesSimulation/00.job/COW Running the command: rm -rf ./work/jobTree Running the command: mkdir ./work/sequenceData Running the command: cactus_createMultiCactusProject.py "/data/home/user010/software/progressiveCactus/work/expTemplate.xml" "./work/progressiveAlignment" --fixNames=0 Running the command: rm -f ./work/cactus.log Running the command: . bin/../src/../environment && cactus_progressive.py --jobTree ./work/jobTree --maxThreads "2" ./work/progressiveAlignment/progressiveAlignment_project.xml --overwrite >> ./work/cactus.log 2>&1
Code:
43435 user010 20 0 9204 1404 1132 S 0.0 0.0 0:00.00 runProgressiveC 43441 user010 20 0 184m 18m 3704 S 0.0 0.0 0:00.40 python 43461 user010 20 0 187m 18m 3676 S 0.0 0.0 0:00.32 python 43462 user010 20 0 0 0 0 Z 0.0 0.0 0:00.00 python <defunct> 43463 user010 20 0 121m 15m 764 S 0.0 0.0 0:00.00 python
- lukas
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