Error log for Relative frequency step

[FrancisNge]

Hi there,

I'm trying to execute DiscoVista with the example data for this command line: $WS_HOME/DiscoVista/src/utils/discoVista.py -a parameters/annotation-1.txt -m 5 -p relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA/ -o relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA/results/anot1 -g Base

Modified to fit the scripts downloaded to my local directory: ./discoVista.py -a /Users/FrancisNge/Documents/SOFTWARE_/DiscoVista_2023_local/2023-04-05-LOCAL/annotation-1.txt -m 5 -p /Users/FrancisNge/Documents/SOFTWARE_/DiscoVista_2023_local/DiscoVista/example/1KP/relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA/ -o /Users/FrancisNge/Documents/SOFTWARE_/DiscoVista_2023_local/DiscoVista/example/1KP/relativeFreq/output -g Base

But half way through the analysis, it stopped. I got the relevant outputs including freqQuad.csv, but am missing the crucial freqQuadCorrected.csv file for the plotting in R.

This was the error log message (attached below): USAGE: [PATH] [annotation] [names] [OUTDIR] [outgroup] outgroup is Base True ['Entransia_fimbriata', 'Klebsormidium_subtile', 'Spirotaenia_minuta', 'Chlorokybus_atmophyticus', 'Mesostigma_viride', 'Uronema_sp', 'Monomastix_opisthostigma', 'Pyramimonas_parkeae', 'Nephroselmis_pyriformis'] Base True ['Penium_margaritaceum', 'Cosmarium_ochthodes', 'Roya_obtusa', 'Netrium_digitus', 'Spirogyra_sp', 'Cylindrocystis_cushleckae', 'Mougeotia_sp', 'Cylindrocystis_brebissonii', 'Mesotaenium_endlicherianum'] Zygnematophyceae True ['Coleochaete_irregularis', 'Coleochaete_scutata', 'Chaetosphaeridium_globosum'] Coleochaetales True ['Catharanthus_roseus', 'Allamanda_cathartica', 'Ipomoea_purpurea', 'Rosmarinus_officinalis', 'Tanacetum_parthenium', 'Inula_helenium', 'Diospyros_malabarica', 'Kochia_scoparia', 'Carica_papaya', 'Arabidopsis_thaliana', 'Hibiscus_cannabinus', 'Populus_trichocarpa', 'Boehmeria_nivea', 'Medicago_truncatula', 'Larrea_tridentata', 'Vitis_vinifera', 'Podophyllum_peltatum', 'Aquilegia_formosa', 'Eschscholzia_californica', 'Sarcandra_glabra', 'Liriodendron_tulipifera', 'Persea_americana', 'Houttuynia_cordata', 'Saruma_henryi', 'Sabal_bermudana', 'Yucca_filamentosa', 'Smilax_bona_nox', 'Colchicum_autumnale', 'Dioscorea_villosa', 'Acorus_americanus', 'Zea_mays', 'Sorghum_bicolor', 'Brachypodium_distachyon', 'Oryza_sativa', 'Kadsura_heteroclita', 'Nuphar_advena', 'Amborella_trichopoda', 'Cunninghamia_lanceolata', 'Juniperus_scopulorum', 'Taxus_baccata', 'Sciadopitys_verticillata', 'Prumnopitys_andina', 'Gnetum_montanum', 'Welwitschia_mirabilis', 'Ephedra_sinica', 'Cedrus_libani', 'Pinus_taeda', 'Cycas_rumphii', 'Cycas_micholitzii', 'Zamia_vazquezii', 'Ginkgo_biloba', 'Psilotum_nudum', 'Ophioglossum_petiolatum', 'Angiopteris_evecta', 'Pteridium_aquilinum', 'Alsophila_spinulosa', 'Equisetum_diffusum', 'Dendrolycopodium_obscurum', 'Pseudolycopodiella_caroliniana', 'Huperzia_squarrosa', 'Selaginella_moellendorffii_1kp', 'Selaginella_moellendorffii_genome', 'Leucodon_brachypus', 'Anomodon_attenuatus', 'Thuidium_delicatulum', 'Rhynchostegium_serrulatum', 'Bryum_argenteum', 'Rosulabryum_cf_capillare', 'Hedwigia_ciliata', 'Ceratodon_purpureus', 'Physcomitrella_patens', 'Polytrichum_commune', 'Sphagnum_lescurii', 'Marchantia_polymorpha', 'Marchantia_emarginata', 'Ricciocarpos_natans', 'Sphaerocarpos_texanus', 'Bazzania_trilobata', 'Metzgeria_crassipilis', 'Nothoceros_aenigmaticus', 'Nothoceros_vincentianus'] Landplants 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 () True /Users/FrancisNge/Documents/SOFTWARE_/DiscoVista_2023_local/DiscoVista/src/utils/display.py /Users/FrancisNge/Documents/SOFTWARE_/DiscoVista_2023_local/DiscoVista/example/1KP/relativeFreq/output/main.tre Base sed: 1: "/Users/FrancisNge/Docum ...": invalid command code F sed: 1: "/Users/FrancisNge/Docum ...": invalid command code F Traceback (most recent call last): File "/Users/FrancisNge/Documents/SOFTWARE_/DiscoVista_2023_local/DiscoVista/src/utils/display.py", line 40, in I.add(int(nd.label.replace("N",""))) ValueError: invalid literal for int() with base 10: "4''"

Any thoughts? 
Thanks in advance
Francis

[FrancisNge]

Hi there, just an update, this error relates to the m1/m2 chips for mac which is incompatible with some of the software dependencies for DiscoVista. I ran the software on a windows and it works.

Francis