Comments (6)
anandksrao
commented on July 28, 2024
1
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: [email protected]
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 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/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
from ltrpred.
HajkD
commented on July 28, 2024
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
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anandksrao
commented on July 28, 2024
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.
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HajkD
commented on July 28, 2024
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
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anandksrao
commented on July 28, 2024
@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: [email protected]
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 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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
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anandksrao
commented on July 28, 2024
@HajkD - hope you can respond to my earlier message, posted above. Thanks in advance
from ltrpred.
Related Issues (20)
- Error in Join solo LTR Copy Number Estimation table HOT 3
- Seeking advice for my test case, test run output validation, and post-processing of files HOT 5
- R installation instructions need to be updated HOT 1
- Installation instructions of dependencies should be updated HOT 4
- Installation of dependencies fail - Docker wrapper needed HOT 9
- License in the repository is missing HOT 1
- Running LTRpred docker container in userspace with udocker HOT 6
- Small details on the vignette HOT 1
- Paper typo HOT 1
- Issue with genome fasta header format
- ltrdigest_complete.fas_DfamAnnotation.out' does not exist HOT 7
- Fasta header truncated in ltrdigest_tabout.csv
- "Error: Tibble columns must have compatible sizes" at Step 6 HOT 2
- Issue with running with singularity HOT 7
- Running LTRPred HOT 3
- Error: Column `cn_3ltr` must be length 48 (the number of rows) or one, not 0 HOT 1
- How to pull LTRpred in singularity HOT 1
- could not install biocLite.R HOT 2
- could LTRpred detect DIRS/DIRS in genome contigs? HOT 3
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