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Old 07-20-2015, 05:33 AM   #1
lukas1848
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Location: Germany

Join Date: Jun 2011
Posts: 54
Default WGA with progressiveCactus

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
Code:
(bin/runProgressiveCactus.sh examples/blanchette00.txt ./work ./work/b00.hal)
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:

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
In addition, I see some idle processes running, which are likely started by progressiveCactus.
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
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

Last edited by lukas1848; 07-21-2015 at 05:37 AM.
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Old 07-20-2015, 07:57 AM   #2
maubp
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Location: Dundee, Scotland, UK

Join Date: Jul 2009
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Default

There certainly are several open issues on the GitHub repository:
https://github.com/glennhickey/progressiveCactus/issues

Did you find one that matched your symptoms?

On the bright side, Glenn Hickey did update the code last month, so it is still being worked on - even if the README file says it is v0.0 (suggesting not really ready for public use).
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Old 07-21-2015, 05:39 AM   #3
lukas1848
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Location: Germany

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Thanks for your response. I followed your advice and started an issue at the github.

https://github.com/glennhickey/progr...ctus/issues/39

I did not find any issues similar to mine there, though.
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Old 07-21-2015, 07:41 AM   #4
maubp
Peter (Biopython etc)
 
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You could add a link on the GitHub issue back to this thread http://seqanswers.com/forums/showthread.php?t=61372

Fingers crossed Glenn can help, or maybe another progressiveCactus user might see this discussion or the issue and be able to help... good luck.
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