Open zyqzyqzyq opened 4 years ago
Hi @zyqzyqzyq
Thank you for contacting me.
The code you refer to isn't an error. It simply returns the solo-LTR copies found with BLAST
: one file using the 3' LTR as BLAST query against the reference genome and one file using the 5' LTR as BLAST query against the reference genome (see Figure 1 for a scheme of 3' and 5' LTRs).
# write estimated solo LTR loci to LTRpred output folder
# this file output includes BLAST hits found with annotated 3' LTRs as BLAST query
cn2bed(
solo.ltr.cn$pred_3ltr,
type = "solo",
filename = paste0(chopped.foldername,"**_soloLTRs_3ltr**"),
output = output.path
)
# this file output includes BLAST hits found with annotated 5' LTRs as BLAST query
cn2bed(
solo.ltr.cn$pred_5ltr,
type = "solo",
filename = paste0(chopped.foldername,"**_solo_LTRs_5ltr**"),
output = output.path
)
The sequences in both files differ, because 3' LTRs and 5' LTRs are not always 100% identical. This is quantified in the LTRpred
output column ltr_similarity
(see here).
So the error Error: Column cn_3ltr must be length 8387 (the number of rows) or one, not 0
must derive from another cause.
Could you please provide me with an example LTRpred
command call in which this error occurs? This will allow me to further troubleshoot.
Many thanks!
Thank you for your answer, this is my LTRpred command call :
library(LTRpred)
setwd = ("/CAT2/zhengyongqiang/escl/default-wenjianjia")
LTRpred(
genome.file = "/CAT2/zhengyongqiang/escl/default-wenjianjia/aaa/G.arboreum_CRI-A2_assembly_v1.0.fasta",
copy.number.est = TRUE,
cores = 20
)
What result in the error Error: Column cn_3ltr must be length 8387 (the number of rows) or one, not 0
Thank you very much !
Ok, I will have a look at this and see if I can reproduce this error.
Hello, @HajkD, I keep getting this error in the Join solo LTR Copy Number Estimation table after Finished LTR CNV estimation
Then , I checked the intermediate files ,find G_soloLTRs_3ltr.bed and G_solo_LTRs_5ltr.bed have a Slight difference (also find in your source code here)
So, if this code mistake result in the error ? thank you!
Best, zyq