Open changchuanjun opened 9 months ago
Hello, Has your problem been resolved? I encountered the same problem. Hope you can help me if you solved this problem.
@qdu-beep ,No, I have not solved this problem. I changed to other pipeline to annotation the gene structure. I used BRAKER3 to annotate my genomes with the RNASeq data and homologous protein data .This is the reference about BRAKER3:
BRAKER3: Fully automated genome annotation using RNA-Seq and protein evidence with GeneMark-ETP, AUGUSTUS and TSEBRA Lars Gabriel, Tomáš Brůna, Katharina J. Hoff, Matthis Ebel, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke bioRxiv 2023.06.10.544449; doi: https://doi.org/10.1101/2023.06.10.544449
same problem
仔细研究了一下,这个报错的原因是缺少consensi.fa.classified这个文件,它本应该在1.RepeatMasker/repeatModeler/RM开头的文件夹中,所以应该去检查RepeatModeler.log。在我的案例中,最后RepeatClassifier的步骤提示Missing Libraries/RepeatPeps.lib.psq。这样一来就明白了,在Libraries里找不到RepeatPeps,导致RepeatModeler无法进行RepeatClassifier,没有生成consensi.fa.classified。
我是通过conda安装的RepeatModeler,它的Libraries默认在conda/share/RepeatModeler里,但是日志里显示在conda/bin里找不到Libraries。所以尝试在bin里添加一个软连接到share/RepeatModeler/Libraries,问题就解决了。
Thanks for your information👍🏻👍🏻👍🏻
---Original--- From: "Cai @.> Date: Wed, Oct 30, 2024 14:24 PM To: @.>; Cc: @.**@.>; Subject: Re: [chenlianfu/geta] error:para_RepeatMasker (Issue #33)
仔细研究了一下,这个报错的原因是缺少consensi.fa.classified这个文件,它本应该在1.RepeatMasker/repeatModeler/RM开头的文件夹中,所以应该去检查RepeatModeler.log。在我的案例中,最后RepeatClassifier的步骤提示Missing Libraries/RepeatPeps.lib.psq。这样一来就明白了,在Libraries里找不到RepeatPeps,导致RepeatModeler无法进行RepeatClassifier,没有生成consensi.fa.classified。
我是通过conda安装的RepeatModeler,它的Libraries默认在conda/share/RepeatModeler里,但是日志里显示在conda/bin里找不到Libraries。所以尝试在bin里添加一个软连接到share/RepeatModeler/Libraries,问题就解决了。
— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>
failed to execute: para_RepeatMasker --out_prefix RepeatModelerout --lib RM/.classified --cpu 4 --tmp_dir para_RepeatMasker.tmp /home/changchuanjun/gene_structure_annotation_20240224/Fuji_Ral-Fuji_Del_20240226/Fuji_Ral_Hap1/out.tmp/genome.fasta &> para_RepeatMasker.log I want to ask how to solve this problem?