HajkD
commented
6 years ago Hi @aset8,
library(LTRpred)
LTRpred(genome.file = "/home/aset/lic.fa", cluster = TRUE, cores = 4)should work.
The command system.file(... , package = "LTRpred") refers only to my example file which is part of the CRAN policy to storing example files in R packages.
The problem of your command run was that LTRpred couldn't find the input files.
I hope this helps.
Best wishes, Hajk
No hmm files were specified, thus the internal HMM library will be used! See '/usr/local/lib/R/site-library/LTRpred/HMMs/hmm_*' for details. No tRNA files were specified, thus the internal tRNA library will be used! See '/usr/local/lib/R/site-library/LTRpred/tRNAs/tRNA_library.fa' for details. Folder '_ltrpred' does not exist yet and will be created... Folder '_ltrpred' exists already and will be used... Starting LTRpred analysis... Step 1: Run LTRharvest... LTRharvest: Generating index file _ltrharvest/_index.fsa with gt suffixerator... gt suffixerator: error: missing argument to option "-db" Running LTRharvest and writing results to _ltrharvest... LTRharvest analysis finished! Step 2: Generating index file _ltrdigest/_index_ltrdigest.fsa with suffixerator... gt suffixerator: error: missing argument to option "-db" LTRdigest: Sort index file... fopen(): cannot open file '_ltrharvest/_Prediction.gff': No such file or directory Running LTRdigest and writing results to _ltrdigest... gt ltrdigest: error: fopen(): cannot open file '_ltrdigest/_index_ltrdigest.fsa.esq': No such file or directory LTRdigest analysis finished! Step 3: Import LTRdigest Predictions... Ошибка: The file '_ltrdigest/-ltrdigest_tabout.csv' does not exist! Please check the correct path or the correct output of LTRharvest() or LTRdigest().
Please, send me detailed instructions for installing and configuring LTRpred
I know how to install dependencies (like, RepeatMasker, HMMER, LTR_harvest and other), but I do not know how to properly configure the paths and freely run the program.
Thanks!