How to fix this run error?

[anandksrao]

Hi,

How may I fix this run error for executing the S. cerevisiae test case, using your LTRpred?

BTW, the 1st test with Hsapiens_ChrY_ltrpred input completed without any error or warning messages. More details below. If you need any additional information, please let me know.

Please help. Thank you, in advance.

PS. I much prefer to use R terminal rather than Docker container etc

R version information (updated just today)

$ R --version
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
https://www.gnu.org/licenses/.

STDOUT of failed test run using downloaded S. cerevisiae genome as input

> Scerevisiae_genome
[1] "_ncbi_downloads/genomes/Saccharomyces_cerevisiae_genomic_refseq.fna.gz"
> LTRpred(
+     genome.file = Scerevisiae_genome,
+     trnas       = paste0(system.file("tRNAs/", package = "LTRpred"),"sacCer3-tRNAs.fa"),
+     hmms        = paste0(system.file("HMMs/", package = "LTRpred"), "hmm_*"),
+     cluster     = TRUE,
+     clust.sim   = 0.9,
+     copy.number.est = TRUE,  
+     cores = 4
+ )
vsearch v2.14.1_macos_x86_64, 8.0GB RAM, 4 cores
https://github.com/torognes/vsearch

Running LTRpred on genome '_ncbi_downloads/genomes/Saccharomyces_cerevisiae_genomic_refseq.fna.gz' with 4 core(s) and searching for retrotransposons using the overlaps option (overlaps = 'no') ...


The output folder '/Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrpred' does not seem to exist yet and will be created ...


LTRpred - Step 1:
Run LTRharvest...
LTRharvest: Generating index file Saccharomyces_cerevisiae_genomic_refseq_ltrharvest/Saccharomyces_cerevisiae_genomic_refseq_index.fsa with gt suffixerator...
Running LTRharvest and writing results to Saccharomyces_cerevisiae_genomic_refseq_ltrharvest...
LTRharvest analysis finished!


LTRpred - Step 2:
Run LTRdigest...
Generating index file Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevisiae_genomic_refseq_index_ltrdigest.fsa with suffixerator...
LTRdigest: Sort index file...
Running LTRdigest and writing results to Saccharomyces_cerevisiae_genomic_refseq_ltrdigest...
LTRdigest analysis finished!


LTRpred - Step 3:
Import LTRdigest Predictions...

Input:  Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevisiae_genomic_refseq_LTRdigestPrediction.gff  -> Row Number:  283
Remove 'NA' -> New Row Number:  283
(1/8) Filtering for repeat regions has been finished.
(2/8) Filtering for LTR retrotransposons has been finished.
(3/8) Filtering for inverted repeats has been finished.
(4/8) Filtering for LTRs has been finished.
(5/8) Filtering for target site duplication has been finished.
(6/8) Filtering for primer binding site has been finished.
(7/8) Filtering for protein match has been finished.
(8/8) Filtering for RR tract has been finished.


LTRpred - Step 4:
Perform ORF Prediction using 'usearch -fastx_findorfs' ...
usearch v11.0.667_i86osx32, 4.0Gb RAM (8.6Gb total), 4 cores
(C) Copyright 2013-18 Robert C. Edgar, all rights reserved.
https://drive5.com/usearch

License: anandksrao@gmail.com

00:00 2.2Mb   100.0% Working

WARNING: Input has lower-case masked sequences

Join ORF Prediction table: nrow(df) = 36 candidates.
unique(ID) = 36 candidates.
unique(orf.id) = 36 candidates.
Perform clustering of similar LTR transposons using 'vsearch --cluster_fast' ...
vsearch v2.14.1_macos_x86_64, 8.0GB RAM, 4 cores
https://github.com/torognes/vsearch

Running CLUSTpred with 90% as sequence similarity threshold using 4 cores ...
vsearch v2.14.1_macos_x86_64, 8.0GB RAM, 4 cores
https://github.com/torognes/vsearch

Reading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrdigest/Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_complete.fas 100%
248182 nt in 36 seqs, min 5189, max 24168, avg 6894
Sorting by length 100%
Counting k-mers 100% 
Clustering 100%  
Sorting clusters 100%
Writing clusters 100% 
Clusters: 10 Size min 1, max 19, avg 3.6
Singletons: 7, 19.4% of seqs, 70.0% of clusters
Sorting clusters by abundance 100%
CLUSTpred output has been stored in: /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/Saccharomyces_cerevisiae_genomic_refseq_ltrpred
Join Cluster table: nrow(df) = 36 candidates.
unique(ID) = 36 candidates.
unique(orf.id) = 36 candidates.
Error: Problem with `summarise()` input `Clust_cn`.
✖ could not find function "n"
ℹ Input `Clust_cn` is `n()`.
ℹ The error occurred in group 1: Clust_Cluster = "cl_3".
Run `rlang::last_error()` to see where the error occurred.
> rlang::last_error()
<error/dplyr_error>
Problem with `summarise()` input `Clust_cn`.
✖ could not find function "n"
ℹ Input `Clust_cn` is `n()`.
ℹ The error occurred in group 1: Clust_Cluster = "cl_3".
Backtrace:
 1. LTRpred::LTRpred(...)
 8. base::.handleSimpleError(...)
 9. dplyr:::h(simpleError(msg, call))
Run `rlang::last_trace()` to see the full context.
> rlang::last_trace()
<error/dplyr_error>
Problem with `summarise()` input `Clust_cn`.
✖ could not find function "n"
ℹ Input `Clust_cn` is `n()`.
ℹ The error occurred in group 1: Clust_Cluster = "cl_3".
Backtrace:
    █
 1. ├─LTRpred::LTRpred(...)
 2. │ ├─dplyr::filter(...)
 3. │ ├─dplyr::summarise(dplyr::group_by(res, Clust_Cluster), Clust_cn = n())
 4. │ └─dplyr:::summarise.grouped_df(...)
 5. │   └─dplyr:::summarise_cols(.data, ...)
 6. │     ├─base::withCallingHandlers(...)
 7. │     └─mask$eval_all_summarise(quo)
 8. └─base::.handleSimpleError(...)
 9.   └─dplyr:::h(simpleError(msg, call))

Session Information

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] LTRpred_1.1.0  devtools_2.3.1 usethis_1.6.1 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5           ape_5.4-1            lattice_0.20-41     
 [4] prettyunits_1.1.1    ps_1.3.4             Biostrings_2.56.0   
 [7] assertthat_0.2.1     rprojroot_1.3-2      digest_0.6.25       
[10] utf8_1.1.4           BiocFileCache_1.12.1 R6_2.4.1            
[13] backports_1.1.8      stats4_4.0.2         RSQLite_2.2.0       
[16] httr_1.4.2           pillar_1.4.6         zlibbioc_1.34.0     
[19] rlang_0.4.7          progress_1.2.2       curl_4.3            
[22] callr_3.4.3          blob_1.2.1           S4Vectors_0.26.1    
[25] desc_1.2.0           downloader_0.4       readr_1.3.1         
[28] stringr_1.4.0        bit_4.0.4            biomaRt_2.44.1      
[31] philentropy_0.4.0    compiler_4.0.2       askpass_1.1         
[34] pkgconfig_2.0.3      BiocGenerics_0.34.0  pkgbuild_1.1.0      
[37] tcltk_4.0.2          openssl_1.4.2        tidyselect_1.1.0    
[40] tibble_3.0.3         IRanges_2.22.2       XML_3.99-0.5        
[43] fansi_0.4.1          dbplyr_1.4.4         crayon_1.3.4        
[46] dplyr_1.0.2          biomartr_0.9.2       withr_2.2.0         
[49] rappdirs_0.3.1       grid_4.0.2           nlme_3.1-148        
[52] lifecycle_0.2.0      DBI_1.1.0            magrittr_1.5        
[55] cli_2.0.2            stringi_1.4.6        XVector_0.28.0      
[58] fs_1.5.0             remotes_2.2.0        testthat_2.3.2      
[61] ellipsis_0.3.1       generics_0.0.2       vctrs_0.3.2         
[64] tools_4.0.2          bit64_4.0.2          Biobase_2.48.0      
[67] glue_1.4.1           purrr_0.3.4          hms_0.5.3           
[70] processx_3.4.3       pkgload_1.1.0        parallel_4.0.2      
[73] AnnotationDbi_1.50.3 BiocManager_1.30.10  sessioninfo_1.1.1   
[76] memoise_1.1.0       

ltrpred_data folder contents

Saccharomyces_cerevisiae_genomic_refseq_ltrpred:
total 464
-rw-r--r--   1 anand  staff   1.3K Aug 20 13:25 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_complete.fas_CLUSTpred.log
-rw-r--r--   1 anand  staff   4.1K Aug 20 13:25 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_complete.fas_CLUSTpred.uc
-rw-r--r--   1 anand  staff   2.7K Aug 20 13:25 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_complete.fas_CLUSTpred.blast6out
drwxr-xr-x   6 anand  staff   192B Aug 20 13:11 .
-rw-r--r--   1 anand  staff   213K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_complete.fas_ORF_prediction_nt.fsa
drwxr-xr-x@ 24 anand  staff   768B Aug 20 13:11 ..

Saccharomyces_cerevisiae_genomic_refseq_ltrdigest:
total 6912
-rw-r--r--   1 anand  staff    28K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq_LTRdigestPrediction.gff
-rw-r--r--   1 anand  staff   248K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_complete.fas
-rw-r--r--   1 anand  staff    16K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_3ltr.fas
-rw-r--r--   1 anand  staff    15K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_5ltr.fas
-rw-r--r--   1 anand  staff   106B Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_ppt.fas
-rw-r--r--   1 anand  staff   112B Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_pbs.fas
-rw-r--r--   1 anand  staff   5.5K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_tabout.csv
-rw-r--r--   1 anand  staff    19K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_pdom_RVT_2.fas
-rw-r--r--   1 anand  staff    27K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_pdom_RVT_2.ali
-rw-r--r--   1 anand  staff   7.1K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_pdom_RVT_2_aa.fas
-rw-r--r--   1 anand  staff    12K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_pdom_rve.fas
-rw-r--r--   1 anand  staff    16K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_pdom_rve.ali
-rw-r--r--   1 anand  staff   4.7K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_pdom_rve_aa.fas
-rw-r--r--   1 anand  staff   522B Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_pdom_RVT_1.fas
-rw-r--r--   1 anand  staff   912B Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_pdom_RVT_1.ali
-rw-r--r--   1 anand  staff   198B Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_pdom_RVT_1_aa.fas
drwxr-xr-x  28 anand  staff   896B Aug 20 13:11 .
-rw-r--r--   1 anand  staff   306B Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_pdom_Retrotrans_gag.fas
-rw-r--r--   1 anand  staff   443B Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_pdom_Retrotrans_gag.ali
-rw-r--r--   1 anand  staff   126B Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_pdom_Retrotrans_gag_aa.fas
-rw-r--r--   1 anand  staff   1.9K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq-ltrdigest_conditions.csv
-rw-r--r--   1 anand  staff   433B Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq_index_ltrdigest.fsa.prj
-rw-r--r--   1 anand  staff    72B Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq_index_ltrdigest.fsa.ssp
-rw-r--r--   1 anand  staff   2.9M Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq_index_ltrdigest.fsa.esq
-rw-r--r--   1 anand  staff   561B Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq_index_ltrdigest.fsa.md5
-rw-r--r--   1 anand  staff   128B Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq_index_ltrdigest.fsa.sds
-rw-r--r--   1 anand  staff   1.3K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq_index_ltrdigest.fsa.des
drwxr-xr-x@ 24 anand  staff   768B Aug 20 13:11 ..

Saccharomyces_cerevisiae_genomic_refseq_ltrharvest:
total 236808
-rw-r--r--   1 anand  staff    21K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq_Prediction_sorted.gff
drwxr-xr-x  16 anand  staff   512B Aug 20 13:11 .
drwxr-xr-x@ 24 anand  staff   768B Aug 20 13:11 ..
-rw-r--r--   1 anand  staff   4.3K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq_Details.tsv
-rw-r--r--   1 anand  staff   222K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq_BetweenLTRSeqs.fsa
-rw-r--r--   1 anand  staff   250K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq_FullLTRretrotransposonSeqs.fsa
-rw-r--r--   1 anand  staff    21K Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq_Prediction.gff
-rw-r--r--   1 anand  staff   4.0M Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq_index.fsa.llv
-rw-r--r--   1 anand  staff    12M Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq_index.fsa.lcp
-rw-r--r--   1 anand  staff   465B Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq_index.fsa.prj
-rw-r--r--   1 anand  staff    93M Aug 20 13:11 Saccharomyces_cerevisiae_genomic_refseq_index.fsa.suf
-rw-r--r--   1 anand  staff    72B Aug 20 13:10 Saccharomyces_cerevisiae_genomic_refseq_index.fsa.ssp
-rw-r--r--   1 anand  staff   2.9M Aug 20 13:10 Saccharomyces_cerevisiae_genomic_refseq_index.fsa.esq
-rw-r--r--   1 anand  staff   561B Aug 20 13:10 Saccharomyces_cerevisiae_genomic_refseq_index.fsa.md5
-rw-r--r--   1 anand  staff   128B Aug 20 13:10 Saccharomyces_cerevisiae_genomic_refseq_index.fsa.sds
-rw-r--r--   1 anand  staff   1.3K Aug 20 13:10 Saccharomyces_cerevisiae_genomic_refseq_index.fsa.des

_ncbi_downloads:
total 0
drwxr-xr-x@ 24 anand  staff   768B Aug 20 13:11 ..
drwxr-xr-x   6 anand  staff   192B Aug 20 13:10 genomes
drwxr-xr-x   3 anand  staff    96B Aug 20 13:10 .

Hsapiens_ChrY_ltrpred:
total 136
drwxr-xr-x@ 24 anand  staff   768B Aug 20 13:11 ..
-rw-r--r--   1 anand  staff   1.4K Aug 20 12:55 Hsapiens_ChrY_LTRpred.bed
-rw-r--r--   1 anand  staff    13K Aug 20 12:55 Hsapiens_ChrY_LTRpred.gff
-rw-r--r--   1 anand  staff    16K Aug 20 12:55 Hsapiens_ChrY_LTRpred_DataSheet.tsv
drwxr-xr-x  12 anand  staff   384B Aug 20 12:55 .
-rw-r--r--   1 anand  staff    11K Aug 20 12:55 Hsapiens_ChrY-ltrdigest_complete.fas_ORF_prediction_nt.fsa
drwxr-xr-x  18 anand  staff   576B Aug 20 12:48 Hsapiens_ChrY_ltrdigest
drwxr-xr-x  15 anand  staff   480B Aug 20 12:47 Hsapiens_ChrY_ltrharvest
-rw-r--r--   1 anand  staff   850B Aug 19 12:30 CLUSTpred.log
-rw-r--r--   1 anand  staff   2.7K Aug 19 12:30 CLUSTpred.uc
-rw-r--r--   1 anand  staff     0B Aug 19 12:11 CLUSTpred.blast6out
-rw-r--r--   1 anand  staff    11K Aug 19 12:11 Hsapiens_ChrY-ltrdigest_complete.fas_nt.fsa

[HajkD]

Hi @anandksrao

Thank you so much for making me aware of this issue.

The bug was a missing dplyr namespace reference to dplyr::n() in the LTRpred::LTRpred() function.

I now pushed this new namespace reference to GitHub and you should now be able to run the tool smoothly.

Please let me know if it works for you now.

Many thanks,
Hajk

[anandksrao]

Thank you @HajkD

Yes, it appears to have worked OK now, after your fix, just one warning, only final few lines of R console STDOUT copy / pasted below:

LTRpred finished all analyses successfully. All output files were stored at '/Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/Sce/ltrpred_data/Dfam/Saccharomyces_cerevisiae_genomic_refseq_ltrpred'.
[1] "Successful job 1 ."
Warning messages:
1: `data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 
2: The LTR copy number estimation returned an empty file. This suggests that there were no solo LTRs found in the input genome sequence

Last time I tried to run LTRpred on a full size genome FASTA input (not human Y chr or yeast genome test runs), usearch's RAM may have been limiting, due to being 32-bit, versus the 64-bit version that is not free-of-cost. And if I remember right, this RAM issue happened for execution on the command line, and also from within Docker and uDocker containers. The containers come with only the 32-bit version, right?

Anyways, I am going to run LTRpred on the full size file again, and will ping you back should I receive any RAM or other errors. I suppose work-arounds to RAM limitations could be one of the following? Any other work arounds that you can think of ?
1. Run LTRpred on individual chromosomes
2. Run on a machine with the 64-bit version of usearch installed on it?

Thank you.

[anandksrao]

I am reporting my run with just 1 chromosome using you LTRpred, on R command line, not via Docker or uDocker.

It ran OK through steps 1 - 6, but returned an error in step 7, as shown below.

Session Info is likely the same as in my previous post, but I am including that as well.

If you'd like to try and replicate my error, here is a link to the input FASTA file, which is only ~ 41MB in size, so not way too larger than one of the test runs using the S. cerevisieae yeast genome ~ 25MB - that executed OK on my machine.

Please let me know if you any other other / missing details to help me troubleshoot my install / run.

Thank you, in advance, @HajkD. Cheers!

Run STDOUT - ONLY 1 chromosome, not full genome

> library(LTRpred)
> LTRpred::LTRpred(genome.file="MtrunA17Chr6.fasta", trnas="MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta",  hmms = paste0(system.file("HMMs/", package = "LTRpred"), "hmm_*"), cluster = TRUE, clust.sim=0.9, copy.number.est=TRUE, cores=4)
vsearch v2.14.1_macos_x86_64, 8.0GB RAM, 4 cores
https://github.com/torognes/vsearch

Running LTRpred on genome 'MtrunA17Chr6.fasta' with 4 core(s) and searching for retrotransposons using the overlaps option (overlaps = 'no') ...


The output folder '/Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrpred' does not seem to exist yet and will be created ...


LTRpred - Step 1:
Run LTRharvest...
LTRharvest: Generating index file MtrunA17Chr6_ltrharvest/MtrunA17Chr6_index.fsa with gt suffixerator...
Running LTRharvest and writing results to MtrunA17Chr6_ltrharvest...
LTRharvest analysis finished!


LTRpred - Step 2:
Run LTRdigest...
Generating index file MtrunA17Chr6_ltrdigest/MtrunA17Chr6_index_ltrdigest.fsa with suffixerator...
LTRdigest: Sort index file...
Running LTRdigest and writing results to MtrunA17Chr6_ltrdigest...
LTRdigest analysis finished!


LTRpred - Step 3:
Import LTRdigest Predictions...

Input:  MtrunA17Chr6_ltrdigest/MtrunA17Chr6_LTRdigestPrediction.gff  -> Row Number:  2500
Remove 'NA' -> New Row Number:  2500
(1/8) Filtering for repeat regions has been finished.
(2/8) Filtering for LTR retrotransposons has been finished.
(3/8) Filtering for inverted repeats has been finished.
(4/8) Filtering for LTRs has been finished.
(5/8) Filtering for target site duplication has been finished.
(6/8) Filtering for primer binding site has been finished.
(7/8) Filtering for protein match has been finished.
(8/8) Filtering for RR tract has been finished.


LTRpred - Step 4:
Perform ORF Prediction using 'usearch -fastx_findorfs' ...
usearch v11.0.667_i86osx32, 4.0Gb RAM (8.6Gb total), 4 cores
(C) Copyright 2013-18 Robert C. Edgar, all rights reserved.
https://drive5.com/usearch

License: anandksrao@gmail.com

00:01 6.3Mb   100.0% Working

WARNING: Input has lower-case masked sequences

Join ORF Prediction table: nrow(df) = 316 candidates.
unique(ID) = 316 candidates.
unique(orf.id) = 316 candidates.
Perform clustering of similar LTR transposons using 'vsearch --cluster_fast' ...
vsearch v2.14.1_macos_x86_64, 8.0GB RAM, 4 cores
https://github.com/torognes/vsearch

Running CLUSTpred with 90% as sequence similarity threshold using 4 cores ...
vsearch v2.14.1_macos_x86_64, 8.0GB RAM, 4 cores
https://github.com/torognes/vsearch

Reading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fasReading file /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fas 100%
3145179 nt in 316 seqs, min 4213, max 25032, avg 9953
Sorting by length 100%
Counting k-mers 100% 
Clustering 100%  
Sorting clusters 100%
Writing clusters 100% 
Clusters: 272 Size min 1, max 13, avg 1.2
Singletons: 255, 80.7% of seqs, 93.8% of clusters
Sorting clusters by abundance 100%
CLUSTpred output has been stored in: /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrpred
Join Cluster table: nrow(df) = 316 candidates.
unique(ID) = 316 candidates.
unique(orf.id) = 316 candidates.
Join Cluster Copy Number table: nrow(df) = 316 candidates.
unique(ID) = 316 candidates.
unique(orf.id)) = 316 candidates.


LTRpred - Step 5:
Perform methylation context quantification..
Join methylation context (CG, CHG, CHH, CCG) count table: nrow(df) = 316 candidates.
unique(ID) = 316 candidates.
unique(orf.id) = 316 candidates.
Copy files to result folder '/Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6_ltrpred'.


LTRpred - Step 6:
Starting retrotransposon evolutionary age estimation by comparing the 3' and 5' LTRs using the molecular evolution model 'K80' and the mutation rate '1.3e-07' (please make sure the mutation rate can be assumed for your species of interest!) for 316 predicted elements ...


Please be aware that evolutionary age estimation based on 3' and 5' LTR comparisons are only very rough time estimates and don't take reverse-transcription mediated retrotransposon recombination between family members of retroelements into account! Please consult Sanchez et al., 2017 Nature Communications and Drost & Sanchez, 2019 Genome Biology and Evolution for more details on retrotransposon recombination.


LTRpred - Step 7:
The LTRpred prediction table has been filtered (default) to remove potential false positives. Predicted LTRs must have an PBS or Protein Domain and must fulfill thresholds: sim = 70%; #orfs = 0. Furthermore, TEs having more than 10% of N's in their sequence have also been removed.
Input #TEs: 316
Output #TEs: 195
Perform solo LTR Copy Number Estimation....
Run makeblastdb of the genome assembly...


Building a new DB, current time: 08/27/2020 18:08:41
New DB name:   /Users/anand/Desktop/Mtr_Nod_TC_Working_Docs/LTRpred/LTRpred_Aug2020/MtruncA17/MtrunA17Chr6.fasta
New DB title:  MtrunA17Chr6.fasta
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 1 sequences in 0.910463 seconds.
Perform BLAST searches of 3' prime LTRs against genome assembly...
Perform BLAST searches of 5' prime LTRs against genome assembly...
Import BLAST results...
Filter hit results...
Estimate CNV for each LTR sequence...
Finished LTR CNV estimation!
Error: Problem with `summarise()` input `cn_3ltr`.
✖ could not find function "n"
ℹ Input `cn_3ltr` is `n()`.
ℹ The error occurred in group 1: query_id = "MtrunA17Chr6_10274850_10286680".
Run `rlang::last_error()` to see where the error occurred.
In addition: Warning message:
`data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 

Session Info

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] LTRpred_1.1.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5          XVector_0.28.0      magrittr_1.5       
 [4] BiocGenerics_0.34.0 hms_0.5.3           zlibbioc_1.34.0    
 [7] IRanges_2.22.2      tidyselect_1.1.0    lattice_0.20-41    
[10] ape_5.4-1           R6_2.4.1            rlang_0.4.7        
[13] fansi_0.4.1         stringr_1.4.0       dplyr_1.0.2        
[16] tools_4.0.2         grid_4.0.2          parallel_4.0.2     
[19] nlme_3.1-149        cli_2.0.2           ellipsis_0.3.1     
[22] assertthat_0.2.1    tibble_3.0.3        lifecycle_0.2.0    
[25] crayon_1.3.4        purrr_0.3.4         readr_1.3.1        
[28] vctrs_0.3.2         S4Vectors_0.26.1    glue_1.4.2         
[31] stringi_1.4.6       compiler_4.0.2      pillar_1.4.6       
[34] generics_0.0.2      Biostrings_2.56.0   stats4_4.0.2       
[37] pkgconfig_2.0.3    

Directory listing after run execution (ending with an error):

MacBook-Pro:MtruncA17 anand$ ls -lRa *
-rw-r--r--  1 anand  staff     124046 Aug 27 14:10 MtrunA17CP.fasta
-rw-r--r--  1 anand  staff    1205197 Aug 27 14:10 MtrunA17Chr0c01.fasta
-rw-r--r--  1 anand  staff     597986 Aug 27 14:10 MtrunA17Chr0c02.fasta
-rw-r--r--  1 anand  staff     275158 Aug 27 14:10 MtrunA17Chr0c03.fasta
-rw-r--r--  1 anand  staff     257650 Aug 27 14:10 MtrunA17Chr0c04.fasta
-rw-r--r--  1 anand  staff     150407 Aug 27 14:10 MtrunA17Chr0c05.fasta
-rw-r--r--  1 anand  staff     113523 Aug 27 14:10 MtrunA17Chr0c06.fasta
-rw-r--r--  1 anand  staff     103643 Aug 27 14:10 MtrunA17Chr0c07.fasta
-rw-r--r--  1 anand  staff      97372 Aug 27 14:10 MtrunA17Chr0c08.fasta
-rw-r--r--  1 anand  staff      63304 Aug 27 14:10 MtrunA17Chr0c09.fasta
-rw-r--r--  1 anand  staff      53406 Aug 27 14:10 MtrunA17Chr0c10.fasta
-rw-r--r--  1 anand  staff      45779 Aug 27 14:10 MtrunA17Chr0c11.fasta
-rw-r--r--  1 anand  staff      43325 Aug 27 14:10 MtrunA17Chr0c12.fasta
-rw-r--r--  1 anand  staff      41558 Aug 27 14:10 MtrunA17Chr0c13.fasta
-rw-r--r--  1 anand  staff      38645 Aug 27 14:10 MtrunA17Chr0c14.fasta
-rw-r--r--  1 anand  staff      36957 Aug 27 14:10 MtrunA17Chr0c15.fasta
-rw-r--r--  1 anand  staff      36855 Aug 27 14:10 MtrunA17Chr0c16.fasta
-rw-r--r--  1 anand  staff      34109 Aug 27 14:10 MtrunA17Chr0c17.fasta
-rw-r--r--  1 anand  staff      33053 Aug 27 14:10 MtrunA17Chr0c18.fasta
-rw-r--r--  1 anand  staff      31618 Aug 27 14:10 MtrunA17Chr0c19.fasta
-rw-r--r--  1 anand  staff      31139 Aug 27 14:10 MtrunA17Chr0c20.fasta
-rw-r--r--  1 anand  staff      30255 Aug 27 14:10 MtrunA17Chr0c21.fasta
-rw-r--r--  1 anand  staff      28328 Aug 27 14:10 MtrunA17Chr0c22.fasta
-rw-r--r--  1 anand  staff      27564 Aug 27 14:10 MtrunA17Chr0c23.fasta
-rw-r--r--  1 anand  staff      27000 Aug 27 14:10 MtrunA17Chr0c24.fasta
-rw-r--r--  1 anand  staff      26799 Aug 27 14:10 MtrunA17Chr0c25.fasta
-rw-r--r--  1 anand  staff      25011 Aug 27 14:10 MtrunA17Chr0c26.fasta
-rw-r--r--  1 anand  staff      24855 Aug 27 14:10 MtrunA17Chr0c27.fasta
-rw-r--r--  1 anand  staff      23830 Aug 27 14:10 MtrunA17Chr0c28.fasta
-rw-r--r--  1 anand  staff      23565 Aug 27 14:10 MtrunA17Chr0c29.fasta
-rw-r--r--  1 anand  staff      23425 Aug 27 14:10 MtrunA17Chr0c30.fasta
-rw-r--r--  1 anand  staff      23309 Aug 27 14:10 MtrunA17Chr0c31.fasta
-rw-r--r--  1 anand  staff      22769 Aug 27 14:10 MtrunA17Chr0c32.fasta
-rw-r--r--  1 anand  staff   56706845 Aug 27 14:10 MtrunA17Chr1.fasta
-rw-r--r--  1 anand  staff   51972594 Aug 27 14:10 MtrunA17Chr2.fasta
-rw-r--r--  1 anand  staff   58931571 Aug 27 14:10 MtrunA17Chr3.fasta
-rw-r--r--  1 anand  staff   64763026 Aug 27 14:10 MtrunA17Chr4.fasta
-rw-r--r--  1 anand  staff   44819633 Aug 27 14:10 MtrunA17Chr5.fasta
-rw-r--r--  1 anand  staff   42866107 Aug 27 14:10 MtrunA17Chr6.fasta
-rw-r--r--  1 anand  staff         13 Aug 27 18:08 MtrunA17Chr6.fasta.nhd
-rw-r--r--  1 anand  staff         65 Aug 27 18:08 MtrunA17Chr6.fasta.nhi
-rw-r--r--  1 anand  staff         75 Aug 27 18:08 MtrunA17Chr6.fasta.nhr
-rw-r--r--  1 anand  staff         96 Aug 27 18:08 MtrunA17Chr6.fasta.nin
-rw-r--r--  1 anand  staff         36 Aug 27 18:08 MtrunA17Chr6.fasta.nog
-rw-r--r--  1 anand  staff         18 Aug 27 18:08 MtrunA17Chr6.fasta.nsd
-rw-r--r--  1 anand  staff         70 Aug 27 18:08 MtrunA17Chr6.fasta.nsi
-rw-r--r--  1 anand  staff   10717033 Aug 27 18:08 MtrunA17Chr6.fasta.nsq
-rw-r--r--  1 anand  staff   56236602 Aug 27 14:10 MtrunA17Chr7.fasta
-rw-r--r--  1 anand  staff   49719286 Aug 27 14:10 MtrunA17Chr8.fasta
-rw-r--r--  1 anand  staff     271631 Aug 27 14:10 MtrunA17MT.fasta
-rw-r--r--  1 anand  staff  437175832 Aug 24 15:38 MtrunA17r5.0-20161119-ANR.genome.fasta
-rw-r--r--  1 anand  staff  437175511 Aug 27 14:08 MtrunA17r5.0-20161119-ANR.genome.fasta.shIDs
-rw-r--r--  1 anand  staff  430008735 Aug 27 14:09 MtrunA17r5.0-20161119-ANR.genome.fasta.shIDscleaned-up
-rw-r--r--  1 anand  staff  430008735 Aug 27 14:09 MtrunA17r5.0-20161119-ANR.genome.fasta.shIDscleaned-up.bak
-rw-r--r--  1 anand  staff     205234 Aug 24 15:37 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta
-rw-r--r--  1 anand  staff     126731 Aug 27 14:23 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.des
-rw-r--r--  1 anand  staff      19456 Aug 27 14:23 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.esq
-rw-r--r--  1 anand  staff      32142 Aug 27 14:23 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.md5
-rw-r--r--  1 anand  staff       2560 Aug 27 14:23 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.ois
-rw-r--r--  1 anand  staff       7784 Aug 27 14:23 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.sds
-rw-r--r--  1 anand  staff       1968 Aug 27 14:23 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.ssp
-rwxr-xr-x  1 anand  staff        944 Aug 27 14:00 fix_multifasta0.pl
-rwxr-xr-x  1 anand  staff       1035 Aug 27 14:00 multifasta2fasta.pl
-rwxr-xr-x  1 anand  staff       1345 Aug 27 14:05 shortenID2.pl

MtrunA17Chr6_ltrpred:
total 17560
drwxr-xr-x  13 anand  staff      416 Aug 27 18:09 .
drwxr-xr-x  69 anand  staff     2208 Aug 27 18:08 ..
-rw-r--r--   1 anand  staff     4373 Aug 27 18:08 MtrunA17Chr6-ltrdigest_complete.fas_CLUSTpred.blast6out
-rw-r--r--   1 anand  staff     1220 Aug 27 18:08 MtrunA17Chr6-ltrdigest_complete.fas_CLUSTpred.log
-rw-r--r--   1 anand  staff    39713 Aug 27 18:08 MtrunA17Chr6-ltrdigest_complete.fas_CLUSTpred.uc
-rw-r--r--   1 anand  staff  1057414 Aug 27 14:24 MtrunA17Chr6-ltrdigest_complete.fas_ORF_prediction_nt.fsa
-rw-r--r--   1 anand  staff    16793 Aug 27 18:08 MtrunA17Chr6_LTRpred.bed
-rw-r--r--   1 anand  staff   195150 Aug 27 18:08 MtrunA17Chr6_LTRpred.gff
-rw-r--r--   1 anand  staff   141179 Aug 27 18:08 MtrunA17Chr6_LTRpred_DataSheet.tsv
drwxr-xr-x  30 anand  staff      960 Aug 27 14:23 MtrunA17Chr6_ltrdigest
drwxr-xr-x  15 anand  staff      480 Aug 27 14:23 MtrunA17Chr6_ltrharvest
-rw-r--r--   1 anand  staff  6211418 Aug 27 18:09 MtrunA17Chr6_soloLTRs_3ltr.bed
-rw-r--r--   1 anand  staff  1299802 Aug 27 18:09 MtrunA17Chr6_solo_LTRs_5ltr.bed

MtrunA17Chr6_ltrpred/MtrunA17Chr6_ltrdigest:
total 30112
drwxr-xr-x  30 anand  staff       960 Aug 27 14:23 .
drwxr-xr-x  13 anand  staff       416 Aug 27 18:09 ..
-rw-r--r--   1 anand  staff    278238 Aug 27 14:24 MtrunA17Chr6-ltrdigest_3ltr.fas
-rw-r--r--   1 anand  staff    278494 Aug 27 14:24 MtrunA17Chr6-ltrdigest_5ltr.fas
-rw-r--r--   1 anand  staff   3207703 Aug 27 14:24 MtrunA17Chr6-ltrdigest_complete.fas
-rw-r--r--   1 anand  staff      1930 Aug 27 14:23 MtrunA17Chr6-ltrdigest_conditions.csv
-rw-r--r--   1 anand  staff      1686 Aug 27 14:24 MtrunA17Chr6-ltrdigest_pbs.fas
-rw-r--r--   1 anand  staff     18560 Aug 27 14:24 MtrunA17Chr6-ltrdigest_pdom_RNase_H.ali
-rw-r--r--   1 anand  staff     11627 Aug 27 14:24 MtrunA17Chr6-ltrdigest_pdom_RNase_H.fas
-rw-r--r--   1 anand  staff      4499 Aug 27 14:24 MtrunA17Chr6-ltrdigest_pdom_RNase_H_aa.fas
-rw-r--r--   1 anand  staff     64745 Aug 27 14:24 MtrunA17Chr6-ltrdigest_pdom_RVT_1.ali
-rw-r--r--   1 anand  staff     37443 Aug 27 14:24 MtrunA17Chr6-ltrdigest_pdom_RVT_1.fas
-rw-r--r--   1 anand  staff     13948 Aug 27 14:24 MtrunA17Chr6-ltrdigest_pdom_RVT_1_aa.fas
-rw-r--r--   1 anand  staff     74120 Aug 27 14:24 MtrunA17Chr6-ltrdigest_pdom_RVT_2.ali
-rw-r--r--   1 anand  staff     56663 Aug 27 14:24 MtrunA17Chr6-ltrdigest_pdom_RVT_2.fas
-rw-r--r--   1 anand  staff     20525 Aug 27 14:24 MtrunA17Chr6-ltrdigest_pdom_RVT_2_aa.fas
-rw-r--r--   1 anand  staff     52959 Aug 27 14:24 MtrunA17Chr6-ltrdigest_pdom_Retrotrans_gag.ali
-rw-r--r--   1 anand  staff     33235 Aug 27 14:24 MtrunA17Chr6-ltrdigest_pdom_Retrotrans_gag.fas
-rw-r--r--   1 anand  staff     13346 Aug 27 14:24 MtrunA17Chr6-ltrdigest_pdom_Retrotrans_gag_aa.fas
-rw-r--r--   1 anand  staff     76227 Aug 27 14:24 MtrunA17Chr6-ltrdigest_pdom_rve.ali
-rw-r--r--   1 anand  staff     53712 Aug 27 14:24 MtrunA17Chr6-ltrdigest_pdom_rve.fas
-rw-r--r--   1 anand  staff     20927 Aug 27 14:24 MtrunA17Chr6-ltrdigest_pdom_rve_aa.fas
-rw-r--r--   1 anand  staff      5085 Aug 27 14:24 MtrunA17Chr6-ltrdigest_ppt.fas
-rw-r--r--   1 anand  staff     56747 Aug 27 14:24 MtrunA17Chr6-ltrdigest_tabout.csv
-rw-r--r--   1 anand  staff    252434 Aug 27 14:24 MtrunA17Chr6_LTRdigestPrediction.gff
-rw-r--r--   1 anand  staff        29 Aug 27 14:23 MtrunA17Chr6_index_ltrdigest.fsa.des
-rw-r--r--   1 anand  staff  10716896 Aug 27 14:23 MtrunA17Chr6_index_ltrdigest.fsa.esq
-rw-r--r--   1 anand  staff        33 Aug 27 14:23 MtrunA17Chr6_index_ltrdigest.fsa.md5
-rw-r--r--   1 anand  staff       438 Aug 27 14:23 MtrunA17Chr6_index_ltrdigest.fsa.prj
-rw-r--r--   1 anand  staff         0 Aug 27 14:23 MtrunA17Chr6_index_ltrdigest.fsa.sds

MtrunA17Chr6_ltrpred/MtrunA17Chr6_ltrharvest:
total 838808
drwxr-xr-x  15 anand  staff        480 Aug 27 14:23 .
drwxr-xr-x  13 anand  staff        416 Aug 27 18:09 ..
-rw-r--r--   1 anand  staff    2675909 Aug 27 14:23 MtrunA17Chr6_BetweenLTRSeqs.fsa
-rw-r--r--   1 anand  staff      33378 Aug 27 14:23 MtrunA17Chr6_Details.tsv
-rw-r--r--   1 anand  staff    3212443 Aug 27 14:23 MtrunA17Chr6_FullLTRretrotransposonSeqs.fsa
-rw-r--r--   1 anand  staff     181606 Aug 27 14:23 MtrunA17Chr6_Prediction.gff
-rw-r--r--   1 anand  staff     181606 Aug 27 14:23 MtrunA17Chr6_Prediction_sorted.gff
-rw-r--r--   1 anand  staff         29 Aug 27 14:17 MtrunA17Chr6_index.fsa.des
-rw-r--r--   1 anand  staff   10716896 Aug 27 14:17 MtrunA17Chr6_index.fsa.esq
-rw-r--r--   1 anand  staff   42866093 Aug 27 14:17 MtrunA17Chr6_index.fsa.lcp
-rw-r--r--   1 anand  staff   26638624 Aug 27 14:17 MtrunA17Chr6_index.fsa.llv
-rw-r--r--   1 anand  staff         33 Aug 27 14:17 MtrunA17Chr6_index.fsa.md5
-rw-r--r--   1 anand  staff        472 Aug 27 14:17 MtrunA17Chr6_index.fsa.prj
-rw-r--r--   1 anand  staff          0 Aug 27 14:17 MtrunA17Chr6_index.fsa.sds
-rw-r--r--   1 anand  staff  342928744 Aug 27 14:17 MtrunA17Chr6_index.fsa.suf

ltrpred_data:
total 0
drwxr-xr-x   4 anand  staff   128 Aug 24 15:55 .
drwxr-xr-x  69 anand  staff  2208 Aug 27 18:08 ..
drwxr-xr-x   7 anand  staff   224 Aug 24 15:45 Dfam
drwxr-xr-x  10 anand  staff   320 Aug 24 17:35 Mtr_genome

ltrpred_data/Dfam:
total 9117064
drwxr-xr-x  7 anand  staff         224 Aug 24 15:45 .
drwxr-xr-x  4 anand  staff         128 Aug 24 15:55 ..
-rw-r--r--  1 anand  staff  1869701327 Jun 18  2019 Dfam.hmm
-rw-r--r--  1 anand  staff   415431599 Aug 24 15:46 Dfam.hmm.h3f
-rw-r--r--  1 anand  staff      705433 Aug 24 15:46 Dfam.hmm.h3i
-rw-r--r--  1 anand  staff   695670696 Aug 24 15:46 Dfam.hmm.h3m
-rw-r--r--  1 anand  staff  1685790183 Aug 24 15:46 Dfam.hmm.h3p

ltrpred_data/Mtr_genome:
total 854728
drwxr-xr-x  10 anand  staff        320 Aug 24 17:35 .
drwxr-xr-x   4 anand  staff        128 Aug 24 15:55 ..
-rw-rw-r--   1 anand  staff  437175832 Dec  1  2016 MtrunA17r5.0-20161119-ANR.genome.fasta
-rw-r--r--   1 anand  staff     205234 Dec 19  2019 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta
-rw-r--r--   1 anand  staff     126731 Aug 24 17:35 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.des
-rw-r--r--   1 anand  staff      19480 Aug 24 17:35 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.esq
-rw-r--r--   1 anand  staff      32142 Aug 24 17:35 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.md5
-rw-r--r--   1 anand  staff       2560 Aug 24 17:35 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.ois
-rw-r--r--   1 anand  staff       7784 Aug 24 17:35 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.sds
-rw-r--r--   1 anand  staff       1968 Aug 24 17:35 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.ssp

[HajkD]

Many thanks for making me aware of this!

There were still two n() without global dplyr:: namespace in the LTRpred() function. I fixed this now and it should work for you now.

Please let me know if it indeed worked on your side as well (after reinstalling LTRpred from the GitHub repo).

Best wishes,
Hajk

[anandksrao]

@HajkD - thank you for your help and support.

Per your suggestion, I re-installed LTRpred and re-ran it with the same input file (M. truncatula PacBio assembled genome from INRA, Toulouse, only Chr #6 ~ 41MB size). And there is real progress in that I obtained multiple output folders and files. Those details are copy / pasted below. I also quickly peeked inside some of the output files, and some of those details are also provided below.

However, my STDOUT on the R command line execution did throw an error, but a different one this time. STDOUT for this run is also copy / pasted below. Along with my R session information (all from command line execution, not Docker or uDocker).

Based on all of these output files / folder, and my observations, I have a few follow-up questions for you. please:

Q1. Is the error message shown below trivial or I can wait for newer but perfect version of LTRpred from you :)

Q2. In the GFF file with intact LTR TEs, when copy number is NA, does that simply mean that there are NO other copies of that LTR sequence at a certain % sequence identity?

Q3. Does the solo LTR file head, tail and # of lines look OK to you? There's only 316 intact LTR-TEs in Chr06 of M. truncatula, but the TSV output file has only 195 entries. What is this numerical difference due to - is it because of filtering, based on default (or stringent) filters?

Q4. The number of solo 3' LTRs and 5' LTRs is 84131 and 17553, which is ~ 3 orders of magnitude of number of intact LTR-TEs. Does this difference counts of intact LTRs vs. solo LTRs seem normal to you, in your experience analyzing several (plant) genomes?

Q5. Does column #5 of solo LTR BED files contain the BLAST scores for DNA sequence matches identified as solo LTRs? The boxplots for the values in column #5 for these 2 files, are shown below, and they show quite some variation, even visualized on a log10 scale:

I look forward to your responses. Thank you very much, in advance - @HajkD.

R command line execution STDOUT & ERROR check

> library(LTRpred)

> LTRpred::LTRpred(genome.file="MtrunA17Chr6.fasta", trnas="MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta",  hmms = paste0(system.file("HMMs/", package = "LTRpred"), "hmm_*"), cluster = TRUE, clust.sim=0.9, copy.number.est=TRUE, cores=4)
vsearch v2.14.1_macos_x86_64, 8.0GB RAM, 4 cores
https://github.com/torognes/vsearch

Running LTRpred on genome 'MtrunA17Chr6.fasta' with 4 core(s) and searching for retrotransposons using the overlaps option (overlaps = 'no') ...


The output folder '/Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrpred' does not seem to exist yet and will be created ...


LTRpred - Step 1:
Run LTRharvest...
LTRharvest: Generating index file MtrunA17Chr6_ltrharvest/MtrunA17Chr6_index.fsa with gt suffixerator...
Running LTRharvest and writing results to MtrunA17Chr6_ltrharvest...
LTRharvest analysis finished!


LTRpred - Step 2:
Run LTRdigest...
Generating index file MtrunA17Chr6_ltrdigest/MtrunA17Chr6_index_ltrdigest.fsa with suffixerator...
LTRdigest: Sort index file...
Running LTRdigest and writing results to MtrunA17Chr6_ltrdigest...
LTRdigest analysis finished!


LTRpred - Step 3:
Import LTRdigest Predictions...

Input:  MtrunA17Chr6_ltrdigest/MtrunA17Chr6_LTRdigestPrediction.gff  -> Row Number:  2500
Remove 'NA' -> New Row Number:  2500
(1/8) Filtering for repeat regions has been finished.
(2/8) Filtering for LTR retrotransposons has been finished.
(3/8) Filtering for inverted repeats has been finished.
(4/8) Filtering for LTRs has been finished.
(5/8) Filtering for target site duplication has been finished.
(6/8) Filtering for primer binding site has been finished.
(7/8) Filtering for protein match has been finished.
(8/8) Filtering for RR tract has been finished.


LTRpred - Step 4:
Perform ORF Prediction using 'usearch -fastx_findorfs' ...
usearch v11.0.667_i86osx32, 4.0Gb RAM (8.6Gb total), 4 cores
(C) Copyright 2013-18 Robert C. Edgar, all rights reserved.
https://drive5.com/usearch

License: anandksrao@gmail.com

00:00 6.3Mb   100.0% Working

WARNING: Input has lower-case masked sequences

Join ORF Prediction table: nrow(df) = 316 candidates.
unique(ID) = 316 candidates.
unique(orf.id) = 316 candidates.
Perform clustering of similar LTR transposons using 'vsearch --cluster_fast' ...
vsearch v2.14.1_macos_x86_64, 8.0GB RAM, 4 cores
https://github.com/torognes/vsearch

Running CLUSTpred with 90% as sequence similarity threshold using 4 cores ...
vsearch v2.14.1_macos_x86_64, 8.0GB RAM, 4 cores
https://github.com/torognes/vsearch

Reading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.faReading file /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrdigest/MtrunA17Chr6-ltrdigest_complete.fas 100%
3145179 nt in 316 seqs, min 4213, max 25032, avg 9953
Sorting by length 100%
Counting k-mers 100% 
Clustering 100%  
Sorting clusters 100%
Writing clusters 100% 
Clusters: 272 Size min 1, max 13, avg 1.2
Singletons: 255, 80.7% of seqs, 93.8% of clusters
Sorting clusters by abundance 100%
CLUSTpred output has been stored in: /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrpred
Join Cluster table: nrow(df) = 316 candidates.
unique(ID) = 316 candidates.
unique(orf.id) = 316 candidates.
Join Cluster Copy Number table: nrow(df) = 316 candidates.
unique(ID) = 316 candidates.
unique(orf.id)) = 316 candidates.


LTRpred - Step 5:
Perform methylation context quantification..
Join methylation context (CG, CHG, CHH, CCG) count table: nrow(df) = 316 candidates.
unique(ID) = 316 candidates.
unique(orf.id) = 316 candidates.
Copy files to result folder '/Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrpred'.


LTRpred - Step 6:
Starting retrotransposon evolutionary age estimation by comparing the 3' and 5' LTRs using the molecular evolution model 'K80' and the mutation rate '1.3e-07' (please make sure the mutation rate can be assumed for your species of interest!) for 316 predicted elements ...


Please be aware that evolutionary age estimation based on 3' and 5' LTR comparisons are only very rough time estimates and don't take reverse-transcription mediated retrotransposon recombination between family members of retroelements into account! Please consult Sanchez et al., 2017 Nature Communications and Drost & Sanchez, 2019 Genome Biology and Evolution for more details on retrotransposon recombination.


LTRpred - Step 7:
The LTRpred prediction table has been filtered (default) to remove potential false positives. Predicted LTRs must have an PBS or Protein Domain and must fulfill thresholds: sim = 70%; #orfs = 0. Furthermore, TEs having more than 10% of N's in their sequence have also been removed.
Input #TEs: 316
Output #TEs: 195
Perform solo LTR Copy Number Estimation....
Run makeblastdb of the genome assembly...


Building a new DB, current time: 09/13/2020 11:34:35
New DB name:   /Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6.fasta
New DB title:  MtrunA17Chr6.fasta
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 1 sequences in 0.651281 seconds.
Perform BLAST searches of 3' prime LTRs against genome assembly...
Perform BLAST searches of 5' prime LTRs against genome assembly...
Import BLAST results...
Filter hit results...
Estimate CNV for each LTR sequence...
Finished LTR CNV estimation!
Join solo LTR Copy Number Estimation table: nrow(df) = 195 candidates.
unique(ID) = 195 candidates.
unique(orf.id) = 195 candidates.
Error: Problem with `mutate()` input `cn_3ltr`.
✖ Input `cn_3ltr` can't be recycled to size 195.
ℹ Input `cn_3ltr` is `ifelse(is.na(cn_3ltr), 0, as.numeric(cn_3ltr))`.
ℹ Input `cn_3ltr` must be size 195 or 1, not 0.
Run `rlang::last_error()` to see where the error occurred.
In addition: Warning message:
`data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 

> rlang::last_error()
<error/dplyr:::mutate_error>
Problem with `mutate()` input `cn_3ltr`.
✖ Input `cn_3ltr` can't be recycled to size 195.
ℹ Input `cn_3ltr` is `ifelse(is.na(cn_3ltr), 0, as.numeric(cn_3ltr))`.
ℹ Input `cn_3ltr` must be size 195 or 1, not 0.
Backtrace:
Run `rlang::last_trace()` to see the full context.

> rlang::last_trace()
<error/dplyr:::mutate_error>
Problem with `mutate()` input `cn_3ltr`.
✖ Input `cn_3ltr` can't be recycled to size 195.
ℹ Input `cn_3ltr` is `ifelse(is.na(cn_3ltr), 0, as.numeric(cn_3ltr))`.
ℹ Input `cn_3ltr` must be size 195 or 1, not 0.
Backtrace:
     █
  1. ├─LTRpred::LTRpred(...)
  2. │ ├─dplyr::mutate(res, cn_3ltr = ifelse(is.na(cn_3ltr), 0, as.numeric(cn_3ltr)))
  3. │ └─dplyr:::mutate.data.frame(...)
  4. │   └─dplyr:::mutate_cols(.data, ...)
  5. │     ├─base::withCallingHandlers(...)
  6. │     └─mask$eval_all_mutate(dots[[i]])
  7. ├─dplyr:::abort_glue(character(0), list(x_size = 0L), "dplyr:::mutate_incompatible_size")
  8. │ ├─rlang::exec(abort, class = class, !!!.envir)
  9. │ └─(function (message = NULL, class = NULL, ..., trace = NULL, parent = NULL, ...
 10. │   └─rlang:::signal_abort(cnd)
 11. │     └─base::signalCondition(cnd)
 12. └─(function (e) ...

> lifecycle::last_warnings()
[[1]]
<deprecated>
message: `data_frame()` is deprecated as of tibble 1.1.0.
Please use `tibble()` instead.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated.
backtrace:
 1. LTRpred::LTRpred(...)
 2. LTRpred::ORFpred(...)
 3. LTRpred::read.orfs(orf.file)
 4. dplyr::data_frame(seq.id = names(SeqFile.table), orfs = as.numeric(SeqFile.table))

Output directory contents

MacBook-Pro:LTRpred_test_13Sep2020 anand$ ls -lhtAR *
-rw-r--r--  1 anand  staff    13B Sep 13 11:34 MtrunA17Chr6.fasta.nhd
-rw-r--r--  1 anand  staff    65B Sep 13 11:34 MtrunA17Chr6.fasta.nhi
-rw-r--r--  1 anand  staff    36B Sep 13 11:34 MtrunA17Chr6.fasta.nog
-rw-r--r--  1 anand  staff    18B Sep 13 11:34 MtrunA17Chr6.fasta.nsd
-rw-r--r--  1 anand  staff    70B Sep 13 11:34 MtrunA17Chr6.fasta.nsi
-rw-r--r--  1 anand  staff    10M Sep 13 11:34 MtrunA17Chr6.fasta.nsq
-rw-r--r--  1 anand  staff    75B Sep 13 11:34 MtrunA17Chr6.fasta.nhr
-rw-r--r--  1 anand  staff    96B Sep 13 11:34 MtrunA17Chr6.fasta.nin
-rw-r--r--  1 anand  staff   2.5K Sep 13 09:06 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.ois
-rw-r--r--  1 anand  staff   1.9K Sep 13 09:06 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.ssp
-rw-r--r--  1 anand  staff    19K Sep 13 09:06 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.esq
-rw-r--r--  1 anand  staff    31K Sep 13 09:06 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.md5
-rw-r--r--  1 anand  staff   7.6K Sep 13 09:06 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.sds
-rw-r--r--  1 anand  staff   124K Sep 13 09:06 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta.des
-rw-r--r--  1 anand  staff    41M Sep 13 08:59 MtrunA17Chr6.fasta
-rw-r--r--  1 anand  staff   410M Sep 13 08:57 MtrunA17r5.0-20161119-ANR.genome.fasta.shIDscleaned-up
-rw-r--r--  1 anand  staff   410M Sep 13 08:55 MtrunA17r5.0-20161119-ANR.genome.fasta.shIDscleaned-up.bak
-rw-r--r--  1 anand  staff   417M Sep 13 08:54 MtrunA17r5.0-20161119-ANR.genome.fasta.shIDs
-rw-r--r--  1 anand  staff   277M Jun  2 08:33 MtrunA17r5.0-ANR-EGN-r1.7.fastaFiles.zip
-rw-r--r--  1 anand  staff   200K Dec 19  2019 MtrunA17r5.0-ANR-EGN-r1.7.trna.fasta

MtrunA17Chr6_ltrpred:
total 17560
-rw-r--r--   1 anand  staff   1.2M Sep 13 11:35 MtrunA17Chr6_solo_LTRs_5ltr.bed
-rw-r--r--   1 anand  staff   5.9M Sep 13 11:35 MtrunA17Chr6_soloLTRs_3ltr.bed
-rw-r--r--   1 anand  staff   138K Sep 13 11:34 MtrunA17Chr6_LTRpred_DataSheet.tsv
-rw-r--r--   1 anand  staff    16K Sep 13 11:34 MtrunA17Chr6_LTRpred.bed
-rw-r--r--   1 anand  staff   191K Sep 13 11:34 MtrunA17Chr6_LTRpred.gff
-rw-r--r--   1 anand  staff   1.1K Sep 13 11:34 MtrunA17Chr6-ltrdigest_complete.fas_CLUSTpred.log
-rw-r--r--   1 anand  staff    39K Sep 13 11:34 MtrunA17Chr6-ltrdigest_complete.fas_CLUSTpred.uc
-rw-r--r--   1 anand  staff   4.3K Sep 13 11:34 MtrunA17Chr6-ltrdigest_complete.fas_CLUSTpred.blast6out
-rw-r--r--   1 anand  staff   1.0M Sep 13 09:07 MtrunA17Chr6-ltrdigest_complete.fas_ORF_prediction_nt.fsa
drwxr-xr-x  30 anand  staff   960B Sep 13 09:06 MtrunA17Chr6_ltrdigest
drwxr-xr-x  15 anand  staff   480B Sep 13 09:06 MtrunA17Chr6_ltrharvest

MtrunA17Chr6_ltrpred/MtrunA17Chr6_ltrdigest:
total 30544
-rw-r--r--  1 anand  staff   247K Sep 13 09:07 MtrunA17Chr6_LTRdigestPrediction.gff
-rw-r--r--  1 anand  staff   3.1M Sep 13 09:07 MtrunA17Chr6-ltrdigest_complete.fas
-rw-r--r--  1 anand  staff   272K Sep 13 09:07 MtrunA17Chr6-ltrdigest_3ltr.fas
-rw-r--r--  1 anand  staff   272K Sep 13 09:07 MtrunA17Chr6-ltrdigest_5ltr.fas
-rw-r--r--  1 anand  staff   5.0K Sep 13 09:07 MtrunA17Chr6-ltrdigest_ppt.fas
-rw-r--r--  1 anand  staff   1.6K Sep 13 09:07 MtrunA17Chr6-ltrdigest_pbs.fas
-rw-r--r--  1 anand  staff    55K Sep 13 09:07 MtrunA17Chr6-ltrdigest_tabout.csv
-rw-r--r--  1 anand  staff    55K Sep 13 09:07 MtrunA17Chr6-ltrdigest_pdom_RVT_2.fas
-rw-r--r--  1 anand  staff    72K Sep 13 09:07 MtrunA17Chr6-ltrdigest_pdom_RVT_2.ali
-rw-r--r--  1 anand  staff    20K Sep 13 09:07 MtrunA17Chr6-ltrdigest_pdom_RVT_2_aa.fas
-rw-r--r--  1 anand  staff    52K Sep 13 09:07 MtrunA17Chr6-ltrdigest_pdom_rve.fas
-rw-r--r--  1 anand  staff    74K Sep 13 09:07 MtrunA17Chr6-ltrdigest_pdom_rve.ali
-rw-r--r--  1 anand  staff    20K Sep 13 09:07 MtrunA17Chr6-ltrdigest_pdom_rve_aa.fas
-rw-r--r--  1 anand  staff    37K Sep 13 09:07 MtrunA17Chr6-ltrdigest_pdom_RVT_1.fas
-rw-r--r--  1 anand  staff    63K Sep 13 09:07 MtrunA17Chr6-ltrdigest_pdom_RVT_1.ali
-rw-r--r--  1 anand  staff    14K Sep 13 09:07 MtrunA17Chr6-ltrdigest_pdom_RVT_1_aa.fas
-rw-r--r--  1 anand  staff    32K Sep 13 09:07 MtrunA17Chr6-ltrdigest_pdom_Retrotrans_gag.fas
-rw-r--r--  1 anand  staff    52K Sep 13 09:07 MtrunA17Chr6-ltrdigest_pdom_Retrotrans_gag.ali
-rw-r--r--  1 anand  staff    13K Sep 13 09:07 MtrunA17Chr6-ltrdigest_pdom_Retrotrans_gag_aa.fas
-rw-r--r--  1 anand  staff    11K Sep 13 09:07 MtrunA17Chr6-ltrdigest_pdom_RNase_H.fas
-rw-r--r--  1 anand  staff    18K Sep 13 09:07 MtrunA17Chr6-ltrdigest_pdom_RNase_H.ali
-rw-r--r--  1 anand  staff   4.4K Sep 13 09:07 MtrunA17Chr6-ltrdigest_pdom_RNase_H_aa.fas
-rw-r--r--  1 anand  staff   1.8K Sep 13 09:06 MtrunA17Chr6-ltrdigest_conditions.csv
-rw-r--r--  1 anand  staff   438B Sep 13 09:06 MtrunA17Chr6_index_ltrdigest.fsa.prj
-rw-r--r--  1 anand  staff    10M Sep 13 09:06 MtrunA17Chr6_index_ltrdigest.fsa.esq
-rw-r--r--  1 anand  staff    33B Sep 13 09:06 MtrunA17Chr6_index_ltrdigest.fsa.md5
-rw-r--r--  1 anand  staff    29B Sep 13 09:06 MtrunA17Chr6_index_ltrdigest.fsa.des
-rw-r--r--  1 anand  staff     0B Sep 13 09:06 MtrunA17Chr6_index_ltrdigest.fsa.sds

MtrunA17Chr6_ltrpred/MtrunA17Chr6_ltrharvest:
total 861064
-rw-r--r--  1 anand  staff   177K Sep 13 09:06 MtrunA17Chr6_Prediction_sorted.gff
-rw-r--r--  1 anand  staff    33K Sep 13 09:06 MtrunA17Chr6_Details.tsv
-rw-r--r--  1 anand  staff   2.6M Sep 13 09:06 MtrunA17Chr6_BetweenLTRSeqs.fsa
-rw-r--r--  1 anand  staff   3.1M Sep 13 09:06 MtrunA17Chr6_FullLTRretrotransposonSeqs.fsa
-rw-r--r--  1 anand  staff   177K Sep 13 09:06 MtrunA17Chr6_Prediction.gff
-rw-r--r--  1 anand  staff    25M Sep 13 09:00 MtrunA17Chr6_index.fsa.llv
-rw-r--r--  1 anand  staff    41M Sep 13 09:00 MtrunA17Chr6_index.fsa.lcp
-rw-r--r--  1 anand  staff   472B Sep 13 09:00 MtrunA17Chr6_index.fsa.prj
-rw-r--r--  1 anand  staff   327M Sep 13 09:00 MtrunA17Chr6_index.fsa.suf
-rw-r--r--  1 anand  staff    10M Sep 13 08:59 MtrunA17Chr6_index.fsa.esq
-rw-r--r--  1 anand  staff    33B Sep 13 08:59 MtrunA17Chr6_index.fsa.md5
-rw-r--r--  1 anand  staff    29B Sep 13 08:59 MtrunA17Chr6_index.fsa.des
-rw-r--r--  1 anand  staff     0B Sep 13 08:59 MtrunA17Chr6_index.fsa.sds

Preliminary and Cursory exploration of some output files / file contents

MacBook-Pro:LTRpred_test_13Sep2020 anand$ cd MtrunA17Chr6_ltrpred/

MacBook-Pro:MtrunA17Chr6_ltrpred anand$ pwd
/Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrpred

MacBook-Pro:MtrunA17Chr6_ltrpred anand$ ls
MtrunA17Chr6-ltrdigest_complete.fas_CLUSTpred.blast6out   MtrunA17Chr6_LTRpred_DataSheet.tsv
MtrunA17Chr6-ltrdigest_complete.fas_CLUSTpred.log         MtrunA17Chr6_ltrdigest
MtrunA17Chr6-ltrdigest_complete.fas_CLUSTpred.uc          MtrunA17Chr6_ltrharvest
MtrunA17Chr6-ltrdigest_complete.fas_ORF_prediction_nt.fsa MtrunA17Chr6_soloLTRs_3ltr.bed
MtrunA17Chr6_LTRpred.bed                                  MtrunA17Chr6_solo_LTRs_5ltr.bed
MtrunA17Chr6_LTRpred.gff

MacBook-Pro:MtrunA17Chr6_ltrpred anand$ wc -l *
      44 MtrunA17Chr6-ltrdigest_complete.fas_CLUSTpred.blast6out
      23 MtrunA17Chr6-ltrdigest_complete.fas_CLUSTpred.log
     588 MtrunA17Chr6-ltrdigest_complete.fas_CLUSTpred.uc
   13569 MtrunA17Chr6-ltrdigest_complete.fas_ORF_prediction_nt.fsa
     316 MtrunA17Chr6_LTRpred.bed
     316 MtrunA17Chr6_LTRpred.gff
     196 MtrunA17Chr6_LTRpred_DataSheet.tsv
wc: MtrunA17Chr6_ltrdigest: read: Is a directory
wc: MtrunA17Chr6_ltrharvest: read: Is a directory
   84131 MtrunA17Chr6_soloLTRs_3ltr.bed
   17553 MtrunA17Chr6_solo_LTRs_5ltr.bed
  116736 total

> file<-file.path("/Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrpred/","MtrunA17Chr6_LTRpred_DataSheet.tsv" )
> MtrunA17Chr6_LTRpred <- read.ltrpred(file)
> dplyr::glimpse(MtrunA17Chr6_LTRpred)
Rows: 195
Columns: 93
$ species                 <chr> "MtrunA17Chr6", "MtrunA17Chr6", "MtrunA17Chr6…
$ ID                      <chr> "MtrunA17Chr6_LTR_retrotransposon1", "MtrunA1…
$ dfam_target_name        <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ ltr_similarity          <dbl> 95.31, 97.55, 98.01, 99.00, 95.69, 90.80, 80.…
$ ltr_age_mya             <dbl> 0.046763367, 0.080002060, 0.019425185, 0.0323…
$ ltr_evo_distance        <dbl> 0.0121584755, 0.0208005356, 0.0050505480, 0.0…
$ similarity              <chr> "(94,96]", "(96,98]", "(98,100]", "(98,100]",…
$ protein_domain          <chr> NA, "rve/RVT_2", "Retrotrans_gag/rve/RVT_2", …
$ orfs                    <int> 0, 1, 2, 2, 1, 0, 0, 0, 2, 2, 4, 4, 2, 3, 0, …
$ chromosome              <chr> "MtrunA17Chr6", "MtrunA17Chr6", "MtrunA17Chr6…
$ start                   <int> 16451, 145489, 530361, 810757, 999563, 125800…
$ end                     <int> 21743, 150193, 535324, 816109, 1004490, 12636…
$ strand                  <chr> "+", "+", "-", "-", "-", "+", "-", "-", "+", …
$ width                   <int> 5293, 4705, 4964, 5353, 4928, 5683, 7832, 947…
$ annotation              <chr> "LTR_retrotransposon", "LTR_retrotransposon",…
$ pred_tool               <chr> "LTRpred", "LTRpred", "LTRpred", "LTRpred", "…
$ frame                   <chr> ".", ".", ".", ".", ".", ".", ".", ".", ".", …
$ score                   <chr> ".", ".", ".", ".", ".", ".", ".", ".", ".", …
$ lLTR_start              <int> 16451, 145489, 530361, 810757, 999563, 125800…
$ lLTR_end                <int> 16701, 145733, 530560, 811354, 999794, 125825…
$ lLTR_length             <int> 251, 245, 200, 598, 232, 250, 230, 178, 194, …
$ rLTR_start              <int> 21488, 149950, 535124, 815511, 1004266, 12634…
$ rLTR_end                <int> 21743, 150193, 535324, 816109, 1004490, 12636…
$ rLTR_length             <int> 256, 244, 201, 599, 225, 247, 226, 173, 184, …
$ lTSD_start              <int> 16446, 145485, 530357, 810753, 999559, 125800…
$ lTSD_end                <int> 16450, 145488, 530360, 810756, 999562, 125800…
$ lTSD_motif              <chr> "ttctt", "tttt", "attt", "atgt", "tctg", "tat…
$ rTSD_start              <int> 21744, 150194, 535325, 816110, 1004491, 12636…
$ rTSD_end                <int> 21748, 150197, 535328, 816113, 1004494, 12636…
$ rTSD_motif              <chr> "ttctt", "tttt", "attt", "atgt", "tctg", "tat…
$ PPT_start               <int> NA, 149939, 530540, NA, NA, NA, NA, NA, NA, N…
$ PPT_end                 <int> NA, 149949, 530556, NA, NA, NA, NA, NA, NA, N…
$ PPT_motif               <chr> NA, "aagggaggaaa", "gttggtgtgagctgtta", NA, N…
$ PPT_strand              <chr> NA, "+", "-", NA, NA, NA, NA, NA, NA, NA, "+"…
$ PPT_offset              <int> NA, 1, 20, NA, NA, NA, NA, NA, NA, NA, 1, 27,…
$ PBS_start               <int> 16701, 145736, NA, NA, NA, 1258261, 1409504, …
$ PBS_end                 <int> 16711, 145747, NA, NA, NA, 1258271, 1409514, …
$ PBS_strand              <chr> "+", "+", NA, NA, NA, "+", "-", "-", NA, NA, …
$ tRNA                    <chr> "MtrunA17_Chr3g0081821 len=65 end=3792184 gn=…
$ tRNA_motif              <chr> "caccatctggg", "tatcaggagcct", NA, NA, NA, "c…
$ PBS_offset              <int> 1, 2, NA, NA, NA, 2, 0, 2, NA, NA, 2, NA, 5, …
$ tRNA_offset             <int> 2, 0, NA, NA, NA, 1, 2, 2, NA, NA, 0, NA, 0, …
$ `PBS/tRNA_edist`        <int> 1, 1, NA, NA, NA, 1, 1, 1, NA, NA, 0, NA, 0, …
$ orf.id                  <chr> "MtrunA17Chr6_16451_21743", "MtrunA17Chr6_145…
$ repeat_region_length    <int> 5303, 4713, 4972, 5361, 4936, 5691, 7840, 948…
$ PPT_length              <int> NA, 11, 17, NA, NA, NA, NA, NA, NA, NA, 13, 1…
$ PBS_length              <int> 11, 12, NA, NA, NA, 11, 11, 11, NA, NA, 12, N…
$ dfam_acc                <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ dfam_bits               <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ dfam_e_value            <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ dfam_bias               <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ `dfam_hmm-st`           <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ `dfam_hmm-en`           <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ dfam_strand             <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ `dfam_ali-st`           <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ `dfam_ali-en`           <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ `dfam_env-st`           <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ `dfam_env-en`           <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ dfam_modlen             <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ dfam_target_description <chr> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ Clust_Cluster           <chr> "unique", "unique", "unique", "unique", "cl_2…
$ Clust_Target            <chr> "none", "none", "none", "none", "MtrunA17Chr6…
$ Clust_Perc_Ident        <dbl> NA, NA, NA, NA, 98.5, NA, NA, NA, NA, NA, NA,…
$ Clust_cn                <int> 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 13, 1, 1, 1,…
$ TE_CG_abs               <dbl> 144, 63, 75, 103, 95, 76, 81, 115, 263, 75, 1…
$ TE_CG_rel               <dbl> 0.027205743, 0.013390011, 0.015108783, 0.0192…
$ TE_CHG_abs              <dbl> 163, 127, 147, 157, 113, 74, 58, 154, 293, 13…
$ TE_CHG_rel              <dbl> 0.030795390, 0.026992561, 0.029613215, 0.0293…
$ TE_CHH_abs              <dbl> 632, 542, 681, 648, 840, 657, 952, 1175, 1607…
$ TE_CHH_rel              <dbl> 0.1194030, 0.1151966, 0.1371878, 0.1210536, 0…
$ TE_CCG_abs              <dbl> 46, 11, 14, 23, 12, 18, 9, 20, 61, 18, 22, 7,…
$ TE_CCG_rel              <dbl> 0.0086907236, 0.0023379384, 0.0028203062, 0.0…
$ TE_N_abs                <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
$ CG_3ltr_abs             <dbl> 20, 1, 0, 5, 0, 5, 4, 4, 0, 1, 12, 14, 44, 74…
$ CG_3ltr_rel             <dbl> 0.078125000, 0.004098361, 0.000000000, 0.0083…
$ CHG_3ltr_abs            <dbl> 17, 7, 5, 13, 1, 4, 1, 2, 4, 5, 51, 46, 13, 9…
$ CHG_3ltr_rel            <dbl> 0.066406250, 0.028688525, 0.025000000, 0.0217…
$ CHH_3ltr_abs            <dbl> 28, 21, 22, 77, 25, 47, 40, 32, 10, 15, 174, …
$ CHH_3ltr_rel            <dbl> 0.10937500, 0.08606557, 0.11000000, 0.1287625…
$ CCG_3ltr_abs            <dbl> 9, 0, 0, 2, 0, 2, 0, 1, 0, 1, 2, 1, 2, 29, 0,…
$ CCG_3ltr_rel            <dbl> 0.0351562500, 0.0000000000, 0.0000000000, 0.0…
$ N_3ltr_abs              <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
$ CG_5ltr_abs             <dbl> 20, 1, 0, 5, 0, 5, 4, 4, 0, 1, 12, 14, 44, 74…
$ CG_5ltr_rel             <dbl> 0.078125000, 0.004098361, 0.000000000, 0.0083…
$ CHG_5ltr_abs            <dbl> 17, 7, 5, 13, 1, 4, 1, 2, 4, 5, 51, 46, 13, 9…
$ CHG_5ltr_rel            <dbl> 0.066406250, 0.028688525, 0.025000000, 0.0217…
$ CHH_5ltr_abs            <dbl> 28, 21, 22, 77, 25, 47, 40, 32, 10, 15, 174, …
$ CHH_5ltr_rel            <dbl> 0.10937500, 0.08606557, 0.11000000, 0.1287625…
$ CCG_5ltr_abs            <dbl> 9, 0, 0, 2, 0, 2, 0, 1, 0, 1, 2, 1, 2, 29, 0,…
$ CCG_5ltr_rel            <dbl> 0.0351562500, 0.0000000000, 0.0000000000, 0.0…
$ N_5ltr_abs              <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, …
$ cn_3ltr                 <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
$ cn_5ltr                 <dbl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…
> MtrunA17Chr6_LTRpred$cn_3ltr
  [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
 [26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
 [51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
 [76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[101] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[126] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[151] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[176] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> MtrunA17Chr6_LTRpred$cn_5ltr
  [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
 [26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
 [51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
 [76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[101] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[126] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[151] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[176] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA

> solo_3ltr = read.table("/Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrpred/MtrunA17Chr6_soloLTRs_3ltr.bed",header=FALSE, sep = "\t")
> summary(solo_3ltr[,5])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   52.8    63.9   102.0   390.4   414.0  6030.0 
> pdf("MtrunA17Chr6_soloLTRs_3ltr_col5_log10_boxplot.pdf")
> boxplot(log10(solo_3ltr[,5]), notch=TRUE, col=c('lightblue'), main="MtrChr06 LTRpred solo 3'LTRs col#5 log10 Boxplot")
> dev.off()

> solo_5ltr = read.table("/Users/anand/Desktop/LTR/LTRpred_test_13Sep2020/MtrunA17Chr6_ltrpred/MtrunA17Chr6_solo_LTRs_5ltr.bed",header=FALSE, sep = "\t")
> summary(solo_5ltr[,5])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   52.8    91.6   174.0   511.7   717.0  5989.0 
> pdf("MtrunA17Chr6_soloLTRs_5ltr_col5_log10_boxplot.pdf")
> boxplot(log10(solo_5ltr[,5]), notch=TRUE, col=c('salmon'), main="MtrChr06 LTRpred solo 5'LTRs col#5 log10 Boxplot")
> dev.off()

Session Information

> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] LTRpred_1.1.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5          XVector_0.28.0      magrittr_1.5       
 [4] BiocGenerics_0.34.0 hms_0.5.3           zlibbioc_1.34.0    
 [7] IRanges_2.22.2      tidyselect_1.1.0    lattice_0.20-41    
[10] ape_5.4-1           R6_2.4.1            rlang_0.4.7        
[13] fansi_0.4.1         stringr_1.4.0       dplyr_1.0.2        
[16] tools_4.0.2         grid_4.0.2          parallel_4.0.2     
[19] nlme_3.1-149        utf8_1.1.4          cli_2.0.2          
[22] ellipsis_0.3.1      assertthat_0.2.1    tibble_3.0.3       
[25] lifecycle_0.2.0     crayon_1.3.4        purrr_0.3.4        
[28] readr_1.3.1         vctrs_0.3.4         S4Vectors_0.26.1   
[31] glue_1.4.2          stringi_1.5.3       compiler_4.0.2     
[34] pillar_1.4.6        generics_0.0.2      Biostrings_2.56.0  
[37] stats4_4.0.2        pkgconfig_2.0.3    

[anandksrao]

@HajkD - hope you can respond to my earlier message, posted above. Thanks in advance