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arendsee / phylostratr

An R framework for phylostratigraphy
GNU General Public License v3.0
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BLAST Database error #17

Open maxnest opened 4 years ago

maxnest commented 4 years ago

Hello! Thank you for such important and useful software. Unfortunately, there was error during the similarity search step. The full code is below:

setwd("/media/sf_Space/Genes/Phylostratr/") library(phylostratr) library(reshape2) library(taxizedb) library(dplyr) library(readr) library(magrittr) focal_taxid <- '981537' strata <- uniprot_strata(focal_taxid, from=1) %>% strata_apply(f=diverse_subtree, n=5, weights=uniprot_weight_by_ref()) %>% use_recommended_prokaryotes %>% add_taxa(c('4932', '9606')) %>% uniprot_fill_strata The focal species is not present in UniProt. You may add it after retrieving uniprot sequences (i.e. with 'uniprot_fill_strata') with a command such as: strata_obj@data$faa[[focal_taxid]] <- '/path/to/your/focal-species.faa' strata@data$faa[[focal_taxid]] <- '/media/sf_Space/Genes/Final_sets_of_sequences/Psimillimum/good.Psimillimum_ref.clustered.genes_level.after_filters.prot.fasta' strata <- add_taxa(strata, "79327") strata@data$faa[["79327"]] <- '/media/sf_Space/Genes/Phylostratr/WormBase_parasites/schmidtea_mediterranea.PRJNA379262.WBPS14.protein.fa' pdf(file="Tree_plot.pdf") strata %>% strata_convert(target='all', to='name') %>% sort_strata %>% plot(cex=0.2, no.margin=TRUE, label.offset=1) dev.off() null device 1
strata <- strata_blast(strata, blast_args=list(nthreads=3)) BLAST Database error: No alias or index file found for protein database [blastdb/4932.faa] in search path [/media/sf_Space/Genes/Phylostratr::] 24932: blasting ...

The fasta file with sequences (4932.faa) exist and located in the /media/sf_Space/Genes/Phylostratr/uniprot-seqs directory. Additional information about system: R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.4 LTS

library(devtools) session_info() ─ Packages ─────────────────────────────────────────────────────────────────── package version date lib source
ape 5.4 2020-06-03 [1] CRAN (R 3.6.3)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.1)
backports 1.1.8 2020-06-17 [1] CRAN (R 3.6.3)
bit 1.1-15.2 2020-02-10 [1] CRAN (R 3.6.3)
bit64 0.9-7 2017-05-08 [1] CRAN (R 3.6.1)
blob 1.2.1 2020-01-20 [1] CRAN (R 3.6.3)
callr 3.4.3 2020-03-28 [1] CRAN (R 3.6.3)
cli 2.0.2 2020-02-28 [1] CRAN (R 3.6.3)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1)
curl 4.3 2019-12-02 [1] CRAN (R 3.6.3)
DBI 1.1.0 2019-12-15 [1] CRAN (R 3.6.3)
dbplyr 1.4.4 2020-05-27 [1] CRAN (R 3.6.3)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.1)
devtools 2.2.1 2019-09-24 [1] CRAN (R 3.6.1)
digest 0.6.25 2020-02-23 [1] CRAN (R 3.6.3)
dplyr 1.0.0 2020-05-29 [1] CRAN (R 3.6.3)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 3.6.3)
fansi 0.4.1 2020-01-08 [1] CRAN (R 3.6.3)
fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.1)
generics 0.0.2 2018-11-29 [1] CRAN (R 3.6.1)
glue 1.4.1 2020-05-13 [1] CRAN (R 3.6.3)
hms 0.5.3 2020-01-08 [1] CRAN (R 3.6.3)
hoardr 0.5.2 2018-12-02 [1] CRAN (R 3.6.3)
lattice 0.20-41 2020-04-02 [4] CRAN (R 3.6.3)
lifecycle 0.2.0 2020-03-06 [1] CRAN (R 3.6.3)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.1)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.1)
nlme 3.1-147 2020-04-13 [4] CRAN (R 3.6.3)
phylostratr 0.2.1 2020-07-09 [1] Github (arendsee/phylostratr@dc1e49a) pillar 1.4.4 2020-05-05 [1] CRAN (R 3.6.3)
pkgbuild 1.0.8 2020-05-07 [1] CRAN (R 3.6.3)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 3.6.1)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 3.6.3)
plyr 1.8.6 2020-03-03 [1] CRAN (R 3.6.3)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 3.6.3)
processx 3.4.3 2020-07-05 [1] CRAN (R 3.6.3)
ps 1.3.3 2020-05-08 [1] CRAN (R 3.6.3)
purrr 0.3.4 2020-04-17 [1] CRAN (R 3.6.3)
R6 2.4.1 2019-11-12 [1] CRAN (R 3.6.3)
rappdirs 0.3.1 2016-03-28 [1] CRAN (R 3.6.3)
Rcpp 1.0.5 2020-07-06 [1] CRAN (R 3.6.3)
readr 1.3.1 2018-12-21 [1] CRAN (R 3.6.1)
remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.1)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 3.6.3)
rlang 0.4.6 2020-05-02 [1] CRAN (R 3.6.3)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.1)
RSQLite 2.2.0 2020-01-07 [1] CRAN (R 3.6.3)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.1)
stringi 1.4.6 2020-02-17 [1] CRAN (R 3.6.3)
stringr 1.4.0 2019-02-10 [1] CRAN (R 3.6.1)
taxizedb 0.1.7.9601 2020-07-09 [1] Github (arendsee/taxizedb@a5a0b5c)
testthat 2.3.2 2020-03-02 [1] CRAN (R 3.6.3)
tibble 3.0.2 2020-07-07 [1] CRAN (R 3.6.3)
tidyselect 1.1.0 2020-05-11 [1] CRAN (R 3.6.3)
usethis * 1.5.1 2019-07-04 [1] CRAN (R 3.6.1)
vctrs 0.3.1 2020-06-05 [1] CRAN (R 3.6.3)
withr 2.2.0 2020-04-20 [1] CRAN (R 3.6.3)

Any help would be appreciated! Thanks

arendsee commented 4 years ago

@maxnest What files are in the blastdb folder?

maxnest commented 4 years ago

@arendsee in the blastdb folder are 3 files: 4932.faa.phr, 4932.faa.pin, and 4932.faa.psq

arendsee commented 4 years ago

@maxnest What's your working directory? If the database files exist, and if R can't find them, then you may be in the wrong directory. Also check your blast database files and the uniprot sequences for files that are empty.