Simon C Chu

Thank you for your reply. Here is the command: ``` singularity exec -B ${WFOLDER}:/home/ -B ${CONFIG}:/opt/LoReAn/third_party/software/augustus/config/ -B ${LIB}:/usr/local/RepeatMasker/Libraries/ ${MODEL}"lorean_latest.sif" lorean \ -pr /home/apple_small.pep.fasta -sp malus_domestica -d -t 16 -kt -sr...

Hi @lfaino , after run without -d option, I still get the same error. Any other suggestions? Thank you a lot!

Also, in the `temporary` folder, there is a file `Final.evm.update.gff3` under folder `run/PASA`. Can I use this as the final results? Thanks in advance!

Hi, the current repeat library is only prepared for human. You need to prepare a library for the plant species that you want to work on. Generally, you need to...

I put a readme to prepare the repeat library here: https://github.com/parklab/xTea/tree/master/xtea/rep_lib_prep. Would you like to have a try? Note, xTea only works for TE insertions of known type, and need...

What do you mean by fasta header format? For which file? The repeatmasker output format is explained here: https://www.repeatmasker.org/webrepeatmaskerhelp.html. To run RepeatMasker on your assembled genome, you need to construct...

You only need to extract the TE type you wanted to work on (each type separately). For example, if you have a repeatmasker output for the whole genome named `species_rmsk.out`,...

Could you try again by replacing `xtea` with `python full-path/x_TEA_main.py` ?

@zhuxf-lab it's based on length for the active Human retrotransposons. For example, L1, I set >5900bp as full length.

@zhuxf-lab I moved your question to a new issue https://github.com/parklab/xTea/issues/50, I'll work on it asap.