nuno-agostinho
commented
1 year ago Hi @verdurin,
Hope you are having a nice day.
It's a bit surprising that it's trying to create cache files, given that the invocation of the installer does not request them.
Your command is not installing VEP cache data, but rather FASTA files: --AUTO af indicates to install updates to the API (a) and to download FASTA files (f) for all species (--SPECIES all).
It seems there is a bug when downloading FASTA files for all species: there is a folder named ancestral_alleles in our FTP server where the FASTA files are located that will raise the error shown because it is not named after any species. For now, if you want to download FASTA files for all species, you will need to indicate the species individually, like so:
perl INSTALL.pl --NO_BIOPERL --NO_HTSLIB --AUTO af --SPECIES acanthochromis_polyacanthus,accipiter_nisus,ailuropoda_melanoleuca,amazona_collaria,amphilophus_citrinellus,amphiprion_ocellaris,amphiprion_percula,anabas_testudineus,anas_platyrhynchos,anas_platyrhynchos_platyrhynchos,anas_zonorhyncha,anolis_carolinensis,anser_brachyrhynchus,anser_cygnoides,aotus_nancymaae,apteryx_haastii,apteryx_owenii,apteryx_rowi,aquila_chrysaetos_chrysaetos,astatotilapia_calliptera,astyanax_mexicanus,astyanax_mexicanus_pachon,athene_cunicularia,balaenoptera_musculus,betta_splendens,bison_bison_bison,bos_grunniens,bos_indicus_hybrid,bos_mutus,bos_taurus,bos_taurus_hybrid,bubo_bubo,buteo_japonicus,caenorhabditis_elegans,cairina_moschata_domestica,calidris_pugnax,calidris_pygmaea,callithrix_jacchus,callorhinchus_milii,camarhynchus_parvulus,camelus_dromedarius,canis_lupus_dingo,canis_lupus_familiaris,canis_lupus_familiarisbasenji,canis_lupus_familiarisboxer,canis_lupus_familiarisgreatdane,canis_lupus_familiarisgsd,capra_hircus,capra_hircus_blackbengal,carassius_auratus,carlito_syrichta,castor_canadensis,catagonus_wagneri,catharus_ustulatus,cavia_aperea,cavia_porcellus,cebus_imitator,cercocebus_atys,cervus_hanglu_yarkandensis,chelonoidis_abingdonii,chelydra_serpentina,chinchilla_lanigera,chlorocebus_sabaeus,choloepus_hoffmanni,chrysemys_picta_bellii,chrysolophus_pictus,ciona_intestinalis,ciona_savignyi,clupea_harengus,colobus_angolensis_palliatus,corvus_moneduloides,cottoperca_gobio,coturnix_japonica,cricetulus_griseus_chok1gshd,cricetulus_griseus_crigri,cricetulus_griseus_picr,crocodylus_porosus,cyanistes_caeruleus,cyclopterus_lumpus,cynoglossus_semilaevis,cyprinodon_variegatus,cyprinus_carpio,cyprinus_carpio_carpio,cyprinus_carpio_germanmirror,cyprinus_carpio_hebaored,cyprinus_carpio_huanghe,danio_rerio,dasypus_novemcinctus,delphinapterus_leucas,denticeps_clupeoides,dicentrarchus_labrax,dipodomys_ordii,dromaius_novaehollandiae,drosophila_melanogaster,echeneis_naucrates,echinops_telfairi,electrophorus_electricus,eptatretus_burgeri,equus_asinus,equus_asinus_asinus,equus_caballus,erinaceus_europaeus,erpetoichthys_calabaricus,erythrura_gouldiae,esox_lucius,falco_tinnunculus,felis_catus,ficedula_albicollis,fukomys_damarensis,fundulus_heteroclitus,gadus_morhua,gallus_gallus,gallus_gallus_gca000002315v5,gallus_gallus_gca016700215v2,gambusia_affinis,gasterosteus_aculeatus,geospiza_fortis,gopherus_agassizii,gopherus_evgoodei,gorilla_gorilla,gouania_willdenowi,haplochromis_burtoni,heterocephalus_glaber_female,heterocephalus_glaber_male,hippocampus_comes,homo_sapiens,hucho_hucho,ictalurus_punctatus,ictidomys_tridecemlineatus,jaculus_jaculus,junco_hyemalis,kryptolebias_marmoratus,labrus_bergylta,larimichthys_crocea,lates_calcarifer,laticauda_laticaudata,latimeria_chalumnae,lepidothrix_coronata,lepisosteus_oculatus,leptobrachium_leishanense,lonchura_striata_domestica,loxodonta_africana,lynx_canadensis,macaca_fascicularis,macaca_mulatta,macaca_nemestrina,malurus_cyaneus_samueli,manacus_vitellinus,mandrillus_leucophaeus,marmota_marmota_marmota,mastacembelus_armatus,maylandia_zebra,meleagris_gallopavo,melopsittacus_undulatus,meriones_unguiculatus,mesocricetus_auratus,microcebus_murinus,microtus_ochrogaster,mola_mola,monodelphis_domestica,monodon_monoceros,monopterus_albus,moschus_moschiferus,mus_caroli,mus_musculus,mus_musculus_129s1svimj,mus_musculus_aj,mus_musculus_akrj,mus_musculus_balbcj,mus_musculus_c3hhej,mus_musculus_c57bl6nj,mus_musculus_casteij,mus_musculus_cbaj,mus_musculus_dba2j,mus_musculus_fvbnj,mus_musculus_lpj,mus_musculus_nodshiltj,mus_musculus_nzohlltj,mus_musculus_pwkphj,mus_musculus_wsbeij,mus_pahari,mus_spicilegus,mus_spretus,mustela_putorius_furo,myotis_lucifugus,myripristis_murdjan,naja_naja,nannospalax_galili,neogobius_melanostomus,neolamprologus_brichardi,neovison_vison,nomascus_leucogenys,notamacropus_eugenii,notechis_scutatus,nothobranchius_furzeri,nothoprocta_perdicaria,numida_meleagris,ochotona_princeps,octodon_degus,oncorhynchus_kisutch,oncorhynchus_mykiss,oncorhynchus_tshawytscha,oreochromis_aureus,oreochromis_niloticus,ornithorhynchus_anatinus,oryctolagus_cuniculus,oryzias_javanicus,oryzias_latipes,oryzias_latipes_hni,oryzias_latipes_hsok,oryzias_melastigma,oryzias_sinensis,otolemur_garnettii,otus_sunia,ovis_aries,ovis_aries_rambouillet,pan_paniscus,pan_troglodytes,panthera_leo,panthera_pardus,panthera_tigris_altaica,papio_anubis,parambassis_ranga,paramormyrops_kingsleyae,parus_major,pavo_cristatus,pelodiscus_sinensis,pelusios_castaneus,periophthalmus_magnuspinnatus,peromyscus_maniculatus_bairdii,petromyzon_marinus,phascolarctos_cinereus,phasianus_colchicus,phocoena_sinus,physeter_catodon,piliocolobus_tephrosceles,podarcis_muralis,poecilia_formosa,poecilia_latipinna,poecilia_mexicana,poecilia_reticulata,pogona_vitticeps,pongo_abelii,procavia_capensis,prolemur_simus,propithecus_coquereli,pseudonaja_textilis,pteropus_vampyrus,pundamilia_nyererei,pygocentrus_nattereri,rattus_norvegicus,rhinolophus_ferrumequinum,rhinopithecus_bieti,rhinopithecus_roxellana,saccharomyces_cerevisiae,saimiri_boliviensis_boliviensis,salarias_fasciatus,salmo_salar,salmo_trutta,salvator_merianae,sander_lucioperca,sarcophilus_harrisii,sciurus_vulgaris,scleropages_formosus,scophthalmus_maximus,serinus_canaria,seriola_dumerili,seriola_lalandi_dorsalis,sinocyclocheilus_anshuiensis,sinocyclocheilus_grahami,sinocyclocheilus_rhinocerous,sorex_araneus,sparus_aurata,spermophilus_dauricus,sphaeramia_orbicularis,sphenodon_punctatus,stachyris_ruficeps,stegastes_partitus,strigops_habroptila,strix_occidentalis_caurina,struthio_camelus_australis,suricata_suricatta,sus_scrofa,sus_scrofa_bamei,sus_scrofa_berkshire,sus_scrofa_hampshire,sus_scrofa_jinhua,sus_scrofa_landrace,sus_scrofa_largewhite,sus_scrofa_meishan,sus_scrofa_pietrain,sus_scrofa_rongchang,sus_scrofa_tibetan,sus_scrofa_usmarc,sus_scrofa_wuzhishan,taeniopygia_guttata,takifugu_rubripes,terrapene_carolina_triunguis,tetraodon_nigroviridis,theropithecus_gelada,tupaia_belangeri,tursiops_truncatus,urocitellus_parryii,ursus_americanus,ursus_maritimus,ursus_thibetanus_thibetanus,varanus_komodoensis,vicugna_pacos,vombatus_ursinus,vulpes_vulpes,xenopus_tropicalis,xiphophorus_couchianus,xiphophorus_maculatus,zalophus_californianus,zonotrichia_albicollis,zosterops_lateralis_melanops --NO_UPDATE --DESTDIR /eb/maint/software/VEP/109-GCC-11.3.0/modules/apiI am sorry for this workaround, but we will try to fix this soon.
Tell me if you still facing issues with this workaround.
Kind regards, Nuno
verdurin
garadar
Describe the issue
I'm working on updating the definition for VEP in EasyBuild, which is a tool for building applications on HPC clusters (https://easybuild.io). The previous definition (107) works fine. I've updated it to 109, changing nothing other than the version of the source file and the associated dependencies, and there is an error that appears to relate to API and/or cache files.
Additional information
Please fill in the following sections to help us find the source of your issue as quickly as possible.
The dependencies are supplied as modules.
System
Full VEP command line
Full error message
It's a bit surprising that it's trying to create cache files, given that the invocation of the installer does not request them. Has something changed here?
I have tried specifying the
cachedirand the same error appears.