joelarmstrong
commented
10 years ago Hi,
The problem is with the tree at the top of the seqfile. Newick trees should have the sibling nodes separated by commas, like so:
(Ostrich, ((Mallard, (Turkey, Chicken)), (Rock_pigeon, ((Common_cuckoo, (Chimney_swift, Anna_s_hummingbird)), (Hoatzin, (Killdeer, (((Emperor_penguin, Adelie_penguin), (Crested_ibis, Little_egret)), ((Peregrine_falcon, (Budgerigar, (Golden_collared_manakin, (American_crow, (Zebra_finch, Medium_ground_finch))))), Downy_woodpecker))))))));
Hope this helps.
vasilislenis
Hello everybody, Finally I managed to install progressiveCactus appropriate. I run the first of the examples and it runs successfully. Now, I'm trying to test it with my data but it complains. It gives me the following errors:
"Error: At least two valid leaf genomes required in input tree
Traceback (most recent call last): File "bin/../src/progressiveCactus.py", line 371, in
sys.exit(main())
File "bin/../src/progressiveCactus.py", line 360, in main
if stage >= 0 and os.path.isdir(workDir):
File "/home/vasilis.lenis/progCactus_ver2/progressiveCactus/python/lib/python2.7/genericpath.py", line 41, in isdir
st = os.stat(s)
TypeError: coercing to Unicode: need string or buffer, neotype found"
The seq file that I'm using is the following:
(Ostrich ((Mallard (Turkey Chicken)) (Rock_pigeon ((Common_cuckoo (Chimney_swift Anna_s_hummingbird)) (Hoatzin (Killdeer (((Emperor_penguin Adelie_penguin) (Crested_ibis Little_egret)) ((Peregrine_falcon (Budgerigar (Golden_collared_manakin (American_crow (Zebra_finch Medium_ground_finch))))) Downy_woodpecker))))))));
Ostrich /home/vasilis.lenis/Multiple_alignments/chicken_Ostrich/ostrich.opt.10kb_gen.fa Mallard /home/vasilis.lenis/Multiple_alignments/chicken_Mallard/duck_gen.fa Turkey /home/vasilis.lenis/Multiple_alignments/chicken_Turkey/melGal1.fa_gen.fa Chicken /home/vasilis.lenis/Multiple_alignments/chicken/chr22.fa Rock_pigeon /home/vasilis.lenis/Multiple_alignments/chicken_Rock_pigeon/pigeon_size_10K_gen.fa Common_cuckoo /home/vasilis.lenis/Multiple_alignments/chicken_Common_cuckoo/cuckoo_10K_gen.fa Chimney_swift /home/vasilis.lenis/Multiple_alignments/chicken_Chimney_swift/swift_10K_gen.fa Anna_s_hummingbird /home/vasilis.lenis/Multiple_alignments/chicken_Anna_s_hummingbird/hummingbird_10K_gen.fa Hoatzin /home/vasilis.lenis/Multiple_alignments/chicken_Hoatzin/hoatzin_size_10K_gen.fa Killdeer /home/vasilis.lenis/Multiple_alignments/chicken_Killdeer/killdeer_10K_gen.fa Emperor_penguin /home/vasilis.lenis/Multiple_alignments/chicken_Emperor_penguin/EPenguin_10K_gen.fa Adelie_penguin /home/vasilis.lenis/Multiple_alignments/chicken_Adelie_penguin/adpenguin_10k_gen.fa Crested_ibis /home/vasilis.lenis/Multiple_alignments/chicken_Crested_ibis/ibis_size_10K_gen.fa Little_egret /home/vasilis.lenis/Multiple_alignments/chicken_Little_egret/egret_size_10K_gen.fa Peregrine_falcon /home/vasilis.lenis/Multiple_alignments/chicken_Peregrine_falcon/falcon_10K_gen.fa Budgerigar /home/vasilis.lenis/Multiple_alignments/chicken_Budgerigar/ap_v6.mega_10K_gen.fa Golden_collared_manakin /home/vasilis.lenis/Multiple_alignments/chicken_Golden_collared_manakin/manakin_size_10K_gen.fa American_crow /home/vasilis.lenis/Multiple_alignments/chicken_American_crow/corvus_scaf_10K_gen.fa Zebra_finch /home/vasilis.lenis/Multiple_alignments/chicken_Zebra_finch/chrom.fa_gen.fa Medium_ground_finch /home/vasilis.lenis/Multiple_alignments/chicken_Medium_ground_finch/geospiza_size_10K_gen.fa Downy_woodpecker /home/vasilis.lenis/Multiple_alignments/chicken_Downy_woodpecker/woodpecker_10K_gen. fa
The command that I'm giving is: bin/runProgressiveCactus.sh ../../MULTIPLE-CACTUS/seqFile-chr22 ./work ./work/testing.hal
I'm really blocked and I cannot find the error that I'm doing. I really need your help…
Thank you in advance, Vasilis.