Relative frequency can't run example and error

[Kekeyang221]

Hi there:

I'm trying to run the frequency and using example file. But something is wrong. I don't know how to solve it. I download this zip file, and add "export WS_HOME=/home/yangk/software" in .bashrc. I have also installed the R packages, like "reshape","reshape2","ggplot2","plyr","scales","ape","optparse" and DendroPy.

My command is "$WS_HOME/DiscoVista/src/utils/discoVista.py -a parameters/annotation-1.txt -m 5 -p relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA/ -o results -g Base".

My linux command line shows error message below: printing errors on results/error.log ['bash', '/home/yangk/software/DiscoVista/src/utils/pos-for-hyp.sh', '/home/yangk/software/DiscoVista/example/1KP/relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA', '/home/yangk/software/DiscoVista/example/1KP/parameters/annotation-1.txt', '/home/yangk/software/DiscoVista/example/1KP/parameters/names.txt', 'results', 'Base'] ['bash', '/home/yangk/software/DiscoVista/src/utils/pos-for-hyp.sh', '/home/yangk/software/DiscoVista/example/1KP/relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA', '/home/yangk/software/DiscoVista/example/1KP/parameters/annotation-1.txt', '/home/yangk/software/DiscoVista/example/1KP/parameters/names.txt', 'results', 'Base']

The generated files in my results shows below: annotation-1.txt annotation-1.txt.with.header.txt astral-job.log error.log estimated_gene_trees.tree estimated_species_tree.tree estimated_species_tree.tree-hypo.tre main-hypo.tre names.txt

My error.log file shows below: USAGE: [PATH] [annotation] [names] [OUTDIR] [outgroup] outgroup is Base True ['Entransia_fimbriata', 'Klebsormidium_subtile', 'Spirotaenia_minuta', 'Chlorokybus_atmophyticus', 'Mesostigma_viride', 'Uronema_sp', 'Mono> True ['Penium_margaritaceum', 'Cosmarium_ochthodes', 'Roya_obtusa', 'Netrium_digitus', 'Spirogyra_sp', 'Cylindrocystis_cushleckae', 'Mougeotia_s> True ['Coleochaete_irregularis', 'Coleochaete_scutata', 'Chaetosphaeridium_globosum'] Coleochaetales True ['Catharanthus_roseus', 'Allamanda_cathartica', 'Ipomoea_purpurea', 'Rosmarinus_officinalis', 'Tanacetum_parthenium', 'Inula_helenium', 'Di> True ['Chara_vulgaris'] Charales All clades specified in the annotation file are monophyletic True Hypo set(['Base', 'Coleochaetales', 'Zygnematophyceae', 'Charales']) ['Base#Charales:2', 'Coleochaetales#Base#Charales:1', 'Zygnematophyceae#Coleochaetales#Base#Charales:1'] Counter({'Base': 1, 'Coleochaetales': 1, 'Zygnematophyceae': 1, 'Landplants': 1, 'Charales': 1}) 3 ()

My astral-job.log file shows below: Error: A JNI error has occurred, please check your installation and try again Exception in thread "main" java.lang.NoClassDefFoundError: phylonet/tree/io/ParseException at java.lang.Class.getDeclaredMethods0(Native Method) at java.lang.Class.privateGetDeclaredMethods(Class.java:2701) at java.lang.Class.privateGetMethodRecursive(Class.java:3048) at java.lang.Class.getMethod0(Class.java:3018) at java.lang.Class.getMethod(Class.java:1784) at sun.launcher.LauncherHelper.validateMainClass(LauncherHelper.java:650) at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:632) Caused by: java.lang.ClassNotFoundException: phylonet.tree.io.ParseException at java.net.URLClassLoader.findClass(URLClassLoader.java:387) at java.lang.ClassLoader.loadClass(ClassLoader.java:418) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) at java.lang.ClassLoader.loadClass(ClassLoader.java:351) ... 7 more

Thank you in advance for any help and I am looking forward to your early reply!