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glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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HAL Export error. converter does not support adding more than one non-leaf:Anc1 #88

Closed malcook closed 6 years ago

malcook commented 6 years ago

Hi. Testing a fresh build of cactus emits a new error when running example:

bin/runProgressiveCactus.sh examples/blanchette00.txt ./test/blanchette00 ./test/blanchette00/b00.hal

Following is relevant tail from cactus.log

2017-10-06 17:46:19.267497: Beginning HAL Export

hal exception caught: Fatal Tree error.  converter does not support adding more than one non-leaf:Anc1

real    0m0.046s
user    0m0.027s
sys 0m0.011s
rm -f ./test/blanchette00/b00.hal
time halAppendCactusSubtree '/home/mec/local/src/progressiveCactus/test/blanchette00/progressiveAlignment/Anc0/Anc0_hal.c2h' '/home/mec/local/src/progressiveCactus/test/blanchette00/progressiveAlignment/Anc0/Anc0_hal.fa' '(Anc1:0.02326,Anc2:0.04)Anc0;' './test/blanchette00/b00.hal'
time halAppendCactusSubtree '/home/mec/local/src/progressiveCactus/test/blanchette00/progressiveAlignment/Anc1/Anc1_hal.c2h' '/home/mec/local/src/progressiveCactus/test/blanchette00/progressiveAlignment/Anc1/Anc1_hal.fa' '((Anc3:0.11,Anc4:0.260342)Anc1:0.02326,Anc2:0.04)Anc0;' './test/blanchette00/b00.hal' --outgroups Anc2
Traceback (most recent call last):
  File "/home/mec/local/src/progressiveCactus/submodules/cactus2hal/bin/cactus2hal.py", line 125, in <module>
    main();
  File "/home/mec/local/src/progressiveCactus/submodules/cactus2hal/bin/cactus2hal.py", line 116, in main
    system(cmdline)
  File "/home/mec/local/src/progressiveCactus/submodules/sonLib/bioio.py", line 185, in system
    raise RuntimeError("Command: %s exited with non-zero status %i" % (command, sts))
RuntimeError: Command: time halAppendCactusSubtree '/home/mec/local/src/progressiveCactus/test/blanchette00/progressiveAlignment/Anc1/Anc1_hal.c2h' '/home/mec/local/src/progressiveCactus/test/blanchette00/progressiveAlignment/Anc1/Anc1_hal.fa' '((Anc3:0.11,Anc4:0.260342)Anc1:0.02326,Anc2:0.04)Anc0;' './test/blanchette00/b00.hal' --outgroups Anc2 exited with non-zero status 1
joelarmstrong commented 6 years ago

Oops, sorry. I pushed a new version of the cactus submodule, which worked for my progressiveCactus install, but I didn't remember I was using newer versions of a lot of the other submodules. I've pushed an update to the cactus2hal submodule which should fix that.

Running:

(in progressiveCactus dir)
git pull
git submodule update --init
make ucsc

should hopefully fix things. Thanks for the bug report!

malcook commented 6 years ago

Fix Confirmed! Running:

runProgressiveCactus.sh --overwrite examples/blanchette00.txt ./test/blanchette00 ./test/blanchette00/msa.hal  --defaultCpu=20  --maxThreads=20  --logInfo --logFile ./test/blanchette00_LOG.txt

....no longer emits error.

Alas, it exposes new issue: #92