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Dfam-consortium / RepeatModeler

De-Novo Repeat Discovery Tool
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Unknown option: ltrstruct #142

Closed ld9866 closed 3 years ago

ld9866 commented 3 years ago

Hello, I used conda to install the related software, but when l gave me the following command, an error would be reported. But when I delete the ltrstruct, it can run normally. What should I do? Good luck！

RepeatModeler -database pig -pa 40 -LTRStruct Unknown option: ltrstruct SYNOPSIS RepeatModeler [-options] -database

DESCRIPTION The options are:

jebrosen commented 3 years ago

RepeatModeler -database pig -pa 40 -LTRStruct Unknown option: ltrstruct

This command line and error message do not match. Did you happen to type it in lowercase (-ltrstruct) instead when you got that error message?

Hello, I used conda to install the related software

There is another problem with this option: bioconda does not currently include NINJA, one of the requirements for using -LTRStruct. There are a few options:

ld9866 commented 3 years ago

The latest version of that container does include NINJA and the other required software for -LTRStruct. Thank you very much for your help. Through the third method you provided, I can now operate normally. It's a great operation.

jebrosen commented 3 years ago

Glad to hear that helped!

Midreancgle commented 2 years ago

Hello,I have the same question.when I run RepeatModeler -database Mo -engine ncbi -pa 20 -LTRStruct >& run.out &,the run.out show LTRPipeline dependency missing or incorrectly set for NINJA_DIR! Rerun ./configure or check your command line to ensure that RepeatModeler has access to and the correct version of this dependency. I used conda to install the NINJA and LtrDeteector, and set up the path to the RepeatModeler and LTRPipeline.I test all the dependent software, LtrDetector、LTR_retriever、MAFFT、CD-HIT、NINJA、LTRHarvest.They all can output the help pages.

`#!/bin/bash

REPEATMODELER_DIR=/home/yue/anaconda3/envs/python27/share/RepeatModeler REPEATMASKER_DIR=/home/yue/anaconda3/envs/python27/share/RepeatMasker ABBLAST_DIR=/home/yue/anaconda3/envs/python27/bin CDHIT_DIR=/home/yue/anaconda3/envs/python27/bin GENOMETOOLS_DIR=/home/yue/anaconda3/envs/python27/bin LTR_RETRIEVER_DIR=/home/yue/anaconda3/envs/python27/bin MAFFT_DIR=/home/yue/anaconda3/envs/python27/bin NINJA_DIR=/home/yue/anaconda3/envs/python27/bin/ RECON_DIR=/home/yue/anaconda3/envs/python27/bin RMBLAST_DIR=/home/yue/anaconda3/envs/python27/bin RSCOUT_DIR=/home/yue/anaconda3/envs/python27/bin TRF_PRGM=/home/yue/anaconda3/envs/python27/bin/trf LTR_DETECTOR_DIR=/home/yue/anaconda3/pkgs/LtrDetector-master/bin export REPEATMODELER_DIR REPEATMASKER_DIR ABBLAST_DIR TRFMASK_DIR CDHIT_DIR GENOMETOOLS_DIR LTR_RETRIEVER_DIR MAFFT_DIR NINJA_DIR RECON_DIR RMBLAST_DIR RSCOUT_DIR TRF_PRGM LTR_DETECTOR_DIR NAME=$(basename $0) perl /home/yue/anaconda3/envs/python27/share/RepeatModeler/${NAME} $@ ~
"RepeatModeler"` Could you give me some help ?Thanks

jebrosen commented 2 years ago

@Midreancgle

I used conda to install the NINJA

To my knowledge, conda/bioconda still does not have a package for NINJA and it needs to be installed and configured separately when installed that way. (the latest version is at: https://github.com/TravisWheelerLab/NINJA/releases/tag/0.98-cluster_only ) . Which conda package for NINJA are you referring to?

Midreancgle commented 2 years ago

Thank you for your help！ I installed version ninja=1.10 by conda before. After seeing your reply, I installed ninja manually and solved the problem about LTRPipeline. But now there is a problem.The same fastq file, the same commands, but the results of multiple runs are different.Can you tell me why this phenomenon occurs?

BuildDatabase -name Mo -engine ncbi genome.fa nohup RepeatModeler -database Mo -engine ncbi -pa 20 -LTRStruct >& run.out & RepeatMasker -lib Mo-families.fa -e ncbi -pa 30 -gff genome.fa

================================================== file name: genome.fa
sequences: 1 total length: 7978604 bp (7969204 bp excl N/X-runs) GC level: 51.23 % bases masked: 1196896 bp ( 15.00 %)

Retroelements 604 740227 bp 9.28 %

LTR elements: 586 692279 bp 8.68 %

DNA transposons 134 173197 bp 2.17 %

Rolling-circles 0 0 bp 0.00 %

Unclassified: 185 196158 bp 2.46 %

Total interspersed repeats: 1109582 bp 13.91 %

Small RNA: 0 0 bp 0.00 %

Satellites: 0 0 bp 0.00 % Simple repeats: 2064 75606 bp 0.95 % Low complexity: 269 11708 bp 0.15 %

================================================== file name: genome.fa
sequences: 1 total length: 7978604 bp (7969204 bp excl N/X-runs) GC level: 51.23 % bases masked: 1193354 bp ( 14.96 %)

Retroelements 659 877753 bp 11.00 %

LTR elements: 599 683874 bp 8.57 %

DNA transposons 92 117452 bp 1.47 %

Rolling-circles 0 0 bp 0.00 %

Unclassified: 215 111266 bp 1.39 %

Total interspersed repeats: 1106471 bp 13.87 %

Small RNA: 0 0 bp 0.00 %

Satellites: 0 0 bp 0.00 % Simple repeats: 2056 75175 bp 0.94 % Low complexity: 269 11708 bp 0.15 %

jebrosen commented 2 years ago

Hi @Midreancgle, I have tried to send a response to this question by email. Here is the message again; I hope this helps to answer:

I am glad to hear your first problem is solved.

The difference in output looks normal; see also https://github.com/Dfam-consortium/RepeatModeler/issues/11. RepeatModeler takes samples of the genome, and not every run is perfectly identical by default. In order to reproduce a specific run of RepeatModeler, the "Random Number Seed" from the program output can be used with the "-srand" option for RepeatModeler.