"phyluce_ncbi_prep_uce_align_files_for_ncbi_targeted_locus_db" creates empty fsa and tbl files

[claudiavaga]

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

[Lavarchus]

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