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halPhyloPMP.py ERROR #302

Closed bright-hu closed 4 months ago

bright-hu commented 4 months ago

Hi, I was running halPhyloPMP.py， the command is halPhyloPMP.py --numProc 100 ../504_way.fish.hal Danio_rerio ../step2/all.mod pick.Danio.wig --targetGenomes Arapaima_gigas,Scleropages_formosus,Megalops_atlanticus,Anguilla_anguilla

but I got “Unrecognized option: --targetGenomes” and lots of halPhyloP help documentation! the “--targetGenomes” option was in the help documentation of halPhyloPMP.py, how to fix this.

Sincerely

bright-hu commented 4 months ago

Also， the final error is multiprocessing.pool.RemoteTraceback: """Traceback (most recent call last): File "/public/home/zhengjiangmin/Software/Python_3.9/lib/python3.9/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/public/home/zhengjiangmin/Software/Python_3.9/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "/public/home/zhengjiangmin/Software/cactus/cactus-bin-v2.5.2/lib/hal/stats/halStats.py", line 27, in runShellCommand raise RuntimeError("Command: %s exited with non-zero status %i" % RuntimeError: Command: halPhyloP ../504_way.fish.hal Danio_rerio ../step2/all.mod pick.Danio_halPhyloPTemp4PF74_0.wig --start 0 --length 16791869 --targetGenomes Arapaima_gigas,Scleropages_formosus,Megalops_atlanticus,Anguilla_anguilla,Clupea_harengus,Chanos_chanos,Sinocyclocheilus_anshuiensis,Cyprinus_carpio,Megalobrama_amblycephala,Electrophorus_electricus,Astyanax_mexicanus,Pygocentrus_nattereri,Esox_lucius,Myripristis_murdjan exited with non-zerostatus 1 """ The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/public/home/zhengjiangmin/Software/cactus/cactus-bin-v2.5.2/bin/halPhyloPMP.py", line 306, in sys.exit(main()) File "/public/home/zhengjiangmin/Software/cactus/cactus-bin-v2.5.2/bin/halPhyloPMP.py", line 303, in main runParallelSlices(args) File "/public/home/zhengjiangmin/Software/cactus/cactus-bin-v2.5.2/bin/halPhyloPMP.py", line 166, in runParallelSlices runParallelShellCommands(sliceCmds, options.numProc) File "/public/home/zhengjiangmin/Software/cactus/cactus-bin-v2.5.2/lib/hal/stats/halStats.py", line 43, in runParallelShellCommands result.get(20000000) File "/public/home/zhengjiangmin/Software/Python_3.9/lib/python3.9/multiprocessing/pool.py", line 771, in get raise self._value RuntimeError: Command: halPhyloP ../504_way.fish.hal Danio_rerio ../step2/all.mod pick.Danio_halPhyloPTemp4PF74_0.wig --start 0 --length 16791869 --targetGenomes Arapaima_gigas,Scleropages_formosus,Megalops_atlanticus,Anguilla_anguilla,Clupea_harengus,Chanos_chanos,Sinocyclocheilus_anshuiensis,Cyprinus_carpio,Megalobrama_amblycephala,Electrophorus_electricus,Astyanax_mexicanus,Pygocentrus_nattereri,Esox_lucius,Myripristis_murdjan exited with non-zero status 1

glennhickey commented 4 months ago

Hi. Unfortunately, halPhyloPMP.py has not been well maintained over the years. I'd like to bring it back, but in the meantime I strongly recommend converting to MAF with cactus-hal2maf and then running PhyloP on the MAF.

bright-hu commented 4 months ago

Thanks anyway.

Glenn Hickey @.***> 于2024年4月29日周一 21:38写道：

Hi. Unfortunately, halPhyloPMP.py has not been well maintained over the years. I'd like to bring it back, but in the meantime I strongly recommend converting to MAF with cactus-hal2maf and then running PhyloP on the MAF.

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