Relative frequency can't run example and error #11
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In the commands you run, instead of "Base" you should use "Outgroup"
because that is the name of the outgroup in this example.
…On Wed, Nov 18, 2020 at 2:27 AM PALADIN168 ***@***.***> wrote:
Hello, this software is very helpful. After installing docker, I try to
run the Relative frequency and using example file. But something is wrong.
I don't know how to solve it.
My error.log file shows below:
USAGE: [PATH] [annotation] [names] [OUTDIR] [outgroup]
outgroup is Base
True ['Amborella_trichopoda'] Amborella
True ['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', 'Penium_margaritaceum', 'Cosmarium_ochthodes',
'Roya_obtusa', 'Netrium_digitus', 'Spirogyra_sp',
'Cylindrocystis_cushleckae', 'Mougeotia_sp', 'Cylindrocystis_brebissonii',
'Mesotaenium_endlicherianum', 'Coleochaete_irregularis',
'Coleochaete_scutata', 'Chaetosphaeridium_globosum', 'Chara_vulgaris',
'Entransia_fimbriata', 'Klebsormidium_subtile', 'Spirotaenia_minuta',
'Chlorokybus_atmophyticus', 'Mesostigma_viride', 'Uronema_sp',
'Monomastix_opisthostigma', 'Pyramimonas_parkeae',
'Nephroselmis_pyriformis'] Outgroup
True ['Sarcandra_glabra'] Chloranthales
True ['Sabal_bermudana', 'Yucca_filamentosa', 'Smilax_bona_nox',
'Colchicum_autumnale', 'Dioscorea_villosa', 'Acorus_americanus',
'Zea_mays', 'Sorghum_bicolor', 'Brachypodium_distachyon', 'Oryza_sativa']
Monocots
True ['Nuphar_advena'] Nuphar
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'] Eudicots
True ['Liriodendron_tulipifera', 'Persea_americana', 'Houttuynia_cordata',
'Saruma_henryi'] Magnoliids
True ['Kadsura_heteroclita'] Kadsura
All clades specified in the annotation file are monophyletic
True
Hypo
set(['Amborella', 'Outgroup', 'Chloranthales', 'Monocots', 'Nuphar',
'Magnoliids', 'Kadsura'])
['Amborella#Outgroup:2', 'Nuphar#Amborella#Outgroup:1',
'Kadsura#Nuphar#Amborella#Outgroup#Monocots:1',
'Kadsura#Nuphar#Amborella#Outgroup:1', 'Chloranthales#Magnoliids:2']
Counter({'Amborella': 1, 'Outgroup': 1, 'Chloranthales': 1, 'Monocots': 1,
'Nuphar': 1, 'Eudicots': 1, 'Magnoliids': 1, 'Kadsura': 1})
3
()
True
/repository/DiscoVista/src/utils/display.py
/data/relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA/results/anot4/main.tre
Base
('Your outgroup species is not found! Please choose outgroup from these
species: ', 'Nuphar, Outgroup, Chloranthales, Monocots, Amborella,
Eudicots, Magnoliids, Kadsura')
------------------------------
And My linux command line shows error message below:
printing errors on
relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA/results/anot4/error.log
['bash', '/repository/DiscoVista/src/utils/pos-for-hyp.sh',
'/data/relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA',
'/data/parameters/annotation-4.txt', '/data/parameters/names.txt',
'relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA/results/anot4',
'Base']
['bash', '/repository/DiscoVista/src/utils/pos-for-hyp.sh',
'/data/relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA',
'/data/parameters/annotation-4.txt', '/data/parameters/names.txt',
'relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA/results/anot4',
'Base']
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Siavash Mirarab
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Is this the example we have packaged? If so, @erfan Sayyari
<esayyari@eng.ucsd.edu> can you check to see if our example is correct?
…On Wed, Nov 18, 2020 at 11:38 AM siavash mirarab ***@***.***> wrote:
In the commands you run, instead of "Base" you should use "Outgroup"
because that is the name of the outgroup in this example.
On Wed, Nov 18, 2020 at 2:27 AM PALADIN168 ***@***.***>
wrote:
> Hello, this software is very helpful. After installing docker, I try to
> run the Relative frequency and using example file. But something is wrong.
> I don't know how to solve it.
>
> My error.log file shows below:
>
> USAGE: [PATH] [annotation] [names] [OUTDIR] [outgroup]
> outgroup is Base
> True ['Amborella_trichopoda'] Amborella
> True ['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', 'Penium_margaritaceum', 'Cosmarium_ochthodes',
> 'Roya_obtusa', 'Netrium_digitus', 'Spirogyra_sp',
> 'Cylindrocystis_cushleckae', 'Mougeotia_sp', 'Cylindrocystis_brebissonii',
> 'Mesotaenium_endlicherianum', 'Coleochaete_irregularis',
> 'Coleochaete_scutata', 'Chaetosphaeridium_globosum', 'Chara_vulgaris',
> 'Entransia_fimbriata', 'Klebsormidium_subtile', 'Spirotaenia_minuta',
> 'Chlorokybus_atmophyticus', 'Mesostigma_viride', 'Uronema_sp',
> 'Monomastix_opisthostigma', 'Pyramimonas_parkeae',
> 'Nephroselmis_pyriformis'] Outgroup
> True ['Sarcandra_glabra'] Chloranthales
> True ['Sabal_bermudana', 'Yucca_filamentosa', 'Smilax_bona_nox',
> 'Colchicum_autumnale', 'Dioscorea_villosa', 'Acorus_americanus',
> 'Zea_mays', 'Sorghum_bicolor', 'Brachypodium_distachyon', 'Oryza_sativa']
> Monocots
> True ['Nuphar_advena'] Nuphar
> 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'] Eudicots
> True ['Liriodendron_tulipifera', 'Persea_americana',
> 'Houttuynia_cordata', 'Saruma_henryi'] Magnoliids
> True ['Kadsura_heteroclita'] Kadsura
> All clades specified in the annotation file are monophyletic
> True
> Hypo
> set(['Amborella', 'Outgroup', 'Chloranthales', 'Monocots', 'Nuphar',
> 'Magnoliids', 'Kadsura'])
> ['Amborella#Outgroup:2', 'Nuphar#Amborella#Outgroup:1',
> 'Kadsura#Nuphar#Amborella#Outgroup#Monocots:1',
> 'Kadsura#Nuphar#Amborella#Outgroup:1', 'Chloranthales#Magnoliids:2']
> Counter({'Amborella': 1, 'Outgroup': 1, 'Chloranthales': 1, 'Monocots':
> 1, 'Nuphar': 1, 'Eudicots': 1, 'Magnoliids': 1, 'Kadsura': 1})
> 3
> ()
> True
> /repository/DiscoVista/src/utils/display.py
> /data/relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA/results/anot4/main.tre
> Base
> ('Your outgroup species is not found! Please choose outgroup from these
> species: ', 'Nuphar, Outgroup, Chloranthales, Monocots, Amborella,
> Eudicots, Magnoliids, Kadsura')
> ------------------------------
>
> And My linux command line shows error message below:
>
> printing errors on
> relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA/results/anot4/error.log
> ['bash', '/repository/DiscoVista/src/utils/pos-for-hyp.sh',
> '/data/relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA',
> '/data/parameters/annotation-4.txt', '/data/parameters/names.txt',
> 'relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA/results/anot4',
> 'Base']
> ['bash', '/repository/DiscoVista/src/utils/pos-for-hyp.sh',
> '/data/relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA',
> '/data/parameters/annotation-4.txt', '/data/parameters/names.txt',
> 'relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA/results/anot4',
> 'Base']
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <#11>, or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AAGJXODS7SH2CTGJP4HCCRTSQOOQ5ANCNFSM4TZY2UGA>
> .
>
--
Siavash Mirarab
--
Siavash Mirarab
|
|
Hi @PALADIN168. Sorry for my late reply. I rerun the example (exact command line from here: https://github.com/esayyari/DiscoVista/tree/master/example#relative-frequency) using both docker and python and they both worked fine. I used this command from the 1KP folder:
Can you please confirm that you still have the same issue? I guess that you should have the results in your output folder: |
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Hello, this software is very helpful. After installing docker, I try to run the Relative frequency and using example file. But something is wrong. I don't know how to solve it.
My error.log file shows below:
USAGE: [PATH] [annotation] [names] [OUTDIR] [outgroup]
outgroup is Base
True ['Amborella_trichopoda'] Amborella
True ['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', 'Penium_margaritaceum', 'Cosmarium_ochthodes', 'Roya_obtusa', 'Netrium_digitus', 'Spirogyra_sp', 'Cylindrocystis_cushleckae', 'Mougeotia_sp', 'Cylindrocystis_brebissonii', 'Mesotaenium_endlicherianum', 'Coleochaete_irregularis', 'Coleochaete_scutata', 'Chaetosphaeridium_globosum', 'Chara_vulgaris', 'Entransia_fimbriata', 'Klebsormidium_subtile', 'Spirotaenia_minuta', 'Chlorokybus_atmophyticus', 'Mesostigma_viride', 'Uronema_sp', 'Monomastix_opisthostigma', 'Pyramimonas_parkeae', 'Nephroselmis_pyriformis'] Outgroup
True ['Sarcandra_glabra'] Chloranthales
True ['Sabal_bermudana', 'Yucca_filamentosa', 'Smilax_bona_nox', 'Colchicum_autumnale', 'Dioscorea_villosa', 'Acorus_americanus', 'Zea_mays', 'Sorghum_bicolor', 'Brachypodium_distachyon', 'Oryza_sativa'] Monocots
True ['Nuphar_advena'] Nuphar
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'] Eudicots
True ['Liriodendron_tulipifera', 'Persea_americana', 'Houttuynia_cordata', 'Saruma_henryi'] Magnoliids
True ['Kadsura_heteroclita'] Kadsura
All clades specified in the annotation file are monophyletic
True
Hypo
set(['Amborella', 'Outgroup', 'Chloranthales', 'Monocots', 'Nuphar', 'Magnoliids', 'Kadsura'])
['Amborella#Outgroup:2', 'Nuphar#Amborella#Outgroup:1', 'Kadsura#Nuphar#Amborella#Outgroup#Monocots:1', 'Kadsura#Nuphar#Amborella#Outgroup:1', 'Chloranthales#Magnoliids:2']
Counter({'Amborella': 1, 'Outgroup': 1, 'Chloranthales': 1, 'Monocots': 1, 'Nuphar': 1, 'Eudicots': 1, 'Magnoliids': 1, 'Kadsura': 1})
3
()
True
/repository/DiscoVista/src/utils/display.py /data/relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA/results/anot4/main.tre
Base
('Your outgroup species is not found! Please choose outgroup from these species: ', 'Nuphar, Outgroup, Chloranthales, Monocots, Amborella, Eudicots, Magnoliids, Kadsura')
And My linux command line shows error message below:
printing errors on relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA/results/anot4/error.log
['bash', '/repository/DiscoVista/src/utils/pos-for-hyp.sh', '/data/relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA', '/data/parameters/annotation-4.txt', '/data/parameters/names.txt', 'relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA/results/anot4', 'Base']
['bash', '/repository/DiscoVista/src/utils/pos-for-hyp.sh', '/data/relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA', '/data/parameters/annotation-4.txt', '/data/parameters/names.txt', 'relativeFreq/astral.trim50genes33taxa.no3rd.final-FNA2AA/results/anot4', 'Base']
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