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error:para_RepeatMasker #33

Open changchuanjun opened 8 months ago

changchuanjun commented 8 months ago

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 1708945984474 I want to ask how to solve this problem?

qdu-beep commented 8 months ago

Hello， Has your problem been resolved? I encountered the same problem. Hope you can help me if you solved this problem.

changchuanjun commented 8 months ago

@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

caiisen commented 1 week ago

same problem

caiisen commented 1 week ago

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。

changchuanjun commented 1 week ago

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。

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