Lavarchus
commented
2 months ago Hi Claudia,
Your folder should contained untrimmed alignments - so just rerun phyluce_align_seqcap_align with the --no-trim flag
Remove locus names from alignment names to keep only species with phyluce_align_remove_locus_name_from_files
You might also want to have a look at your nexus files to see if your alignments are interleaved.
Hope this helps to fix your issue!
Best fishes
Hi,
I am having trouble running phyluce_ncbi_prep_uce_align_files_for_ncbi_targeted_locus_db.
Seems to not run into an error, but it creates empty fsa and tbl files. I am using the path to my mafft-nexus-internal-trimmed/ folder and this is the ncbi.conf file that I am using:
[metadata] molecule:DNA moltype:genomic specimen_voucher:{} bioproject:PRJNA1071668 biosample:{}
[organisms] Cryptotrochus_brevipalus_LIB49_B9:Cryptotrochus brevipalus Cyathotrochus_pileus_IGS109:Cyathotrochus pileus Deltocyathus_cameratus_DNA62:Deltocyathus cameratus Deltocyathus_heteroclitus_CFV123:Deltocyathus heteroclitus Deltocyathus_magnificus_IGS128:Deltocyathus magnificus Deltocyathus_rotulus_IGS129:Deltocyathus rotulus Deltocyathus_suluensis_CFV111:Deltocyathus suluensis Notocyathus_venustus_LIB42_A6:Notocyathus venustus Thrypticotrochus_petterdi_CFV160:Thrypticotrochus petterdi Tropidocyathus_labidus_IGS123:Tropidocyathus labidus
[biosamples] Cryptotrochus_brevipalus_LIB49_B9:SAMN39709812 Cyathotrochus_pileus_IGS109:SAMN39709813 Deltocyathus_cameratus_DNA62:SAMN39709814 Deltocyathus_heteroclitus_CFV123:SAMN39709815 Deltocyathus_magnificus_IGS128:SAMN39709816 Deltocyathus_rotulus_IGS129:SAMN39709817 Deltocyathus_suluensis_CFV111:SAMN39709818 Notocyathus_venustus_LIB42_A6:SAMN39709819 Thrypticotrochus_petterdi_CFV160:SAMN39709820 Tropidocyathus_labidus_IGS123:SAMN39709821
[vouchers] Cryptotrochus_brevipalus_LIB49_B9:MNHN:LIB49_B9 Cyathotrochus_pileus_IGS109:MNHN:IGS109 Deltocyathus_cameratus_DNA62:MNHN:DNA62 Deltocyathus_heteroclitus_CFV123:MNHN:CFV123 Deltocyathus_magnificus_IGS128:MNHN:IGS128 Deltocyathus_rotulus_IGS129:MNHN:IGS129 Deltocyathus_suluensis_CFV111:MNHN:CFV111 Notocyathus_venustus_LIB42_A6:MNHN:LIB42_A6 Thrypticotrochus_petterdi_CFV160:MHNH:CFV160 Tropidocyathus_labidus_IGS123:MNHN:IGS123
[exclude taxa] Acropora_digitifera_ReFuGe Acropora_hyacinthus_ReFuGe Acropora_millepora_REL_ReFuGe Acropora_muricata_ANT13 Acropora_palmata_ANT163 Agaricia_lamarcki_ANT164 Alveopora_japonica_Ryu_2019 Astrangia_sp_DNA45 Astreopora_expansa_REL_ReFuGe Balanophyllia_elegans_ANT185 Caryophyllia_scobinosa_IGS119 Corallimorphus_profundus_ANT274 Corynactis_chilensis_ANT1 Dendrogyra_cylindrus_ANT168 Dendrophyllia_sp_transK_ReFuGe Desmophyllum_pertusum_IGS036 Discosoma_carlgreni_ANT3 Discosoma_santahelenae_ANT153 Eguchipsammia_fistula_transK_ReFuGe Enallopsammia_profunda_ANT283 Enallopsammia_rostrata_ANT212 Favia_fragum_ANT161 Fimbriaphyllia_ancora_REL_ReFuGe Flabellum_alabastrum_ANT96 Galaxea_astreata_REL_ReFuGe Goniopora_columna_REL_ReFuGe Lobophyllia_radians_REL_ReFuGe Madrepora_oculata_ANT281 Meandrina_meandrites_ANT162 Montastraea_cavernosa_refuge Montipora_aequituberculata_Kenkel_2017 Mussismilia_hispida_ANT120 Oculina_patagonica_ANT192 Oculina_robusta_ANT197 Oculina_varicosa_ANT182 Orbicella_annularis_ANT166 Orbicella_faveolata_ReFuGe Paraconotrochus_antarcticus_ANT286 Pavona_decussata_ANT18 Platygyra_carnosa_ReFuGe Platygyra_sinensis_REL_ReFuGe Pocillopora_damicornis_ANT16 Porites_divaricata_ANT196 Porites_evermanni_ANT265 Porites_lobata_ANT240 Porites_lutea_ANT269 Porites_panamensis_ANT186 Ricordea_florida_ANT154 Seriatopora_hystrix_ReFuGe Siderastrea_siderans_ANT165 Stylophora_pistillata_ANT17 Thecopsammia_sp_ANT284 Turbinaria_mesenterina_REL_ReFuGe
Could someone help me understand if I am doing something wrong?
Thank you very much in advance, Claudia