【更新】七月上旬更新日志

近期博客更新在https://abysw.github.io

 

 

简要内容总结如下：

orthofinder打开文件数上限

【问题】打开文件数上限过少
【报错】ERROR: The system limits on the number of files a process can open is too low. For 58 species OrthoFinder needs to be able to open at least r=3464 files. Please increase the limit and restart OrthoFinder

远程桌面访问linux

目的：使用台式机的Windows远程桌面，访问linux系统的集群。
台式机：win11
服务器：centos7.9

基因功能注释笔记

 

arm服务器安装samtools

通过局域网共享网络连接（测试版）

 

EVM基因注释整合

EVidenceModeler
conda install -c bioconda evidencemodeler
conda install -c bioconda/label/cf201901 evidencemodeler

按例子跑一下：
/abysw/app/miniconda3/envs/evm/opt/evidencemodeler-1.1.1/simple_example

Can’t locate URI/Escape.pm in @INC
conda update evidencemodeler

坏掉的maker

Possible precedence issue with control flow operator at /xulab/pipeline/app/miniconda3/envs/maker/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.

MAKER version 2.31.11

原因描述很简单，就是说perl的东西坏了。

The problem is the bioperl or even perl installation —> “Possible precedence issue with control flow operator at /apps/maker/3.01.03/lib/site_perl/5.26.2/Bio/DB/IndexedBase.pm line 805.”

You may have a custom install of perl without BerkleyDB setup, or need to update BioPerl. If you installed MAKER with MiniConda, then it tried to setup a custom perl and BioPerl that is broken. You probably need to reinstall MAKER. Using the system perl may be the easiest.

—Carson

https://groups.google.com/g/maker-devel/c/T9NSb8cYjUQ

busco报错

本文需要解决的问题：
2022-06-09 16:05:13 INFO: ***** Start a BUSCO v5.3.0 analysis, current time: 06/09/2022 16:05:13 *****
2022-06-09 16:05:13 INFO: Configuring BUSCO with local environment
2022-06-09 16:05:13 INFO: Mode is proteins
2022-06-09 16:05:13 INFO: ‘Force’ option selected; overwriting previous results directory
2022-06-09 16:05:13 INFO: Downloading information on latest versions of BUSCO data…
2022-06-09 16:07:20 ERROR: Cannot reach https://busco-data.ezlab.org/v5/data/file_versions.tsv
2022-06-09 16:07:20 ERROR: BUSCO analysis failed !
2022-06-09 16:07:20 ERROR: Check the logs, read the user guide (https://busco.ezlab.org/busco_userguide.html), and check the BUSCO issue board on https://gitlab.com/ezlab/busco/issues

报错原因是网站服务器不稳定，尝试修改了代码和配置，均无效（需要动的代码有点多）。

APA分析TAPIS

APA分析的工具TAPIS，需要注意修改部分脚本，主要注意事项如下：

1. 所依赖的python版本为2.7；
2. fasta用非压缩文件时，需要修改代码；
3. 所使用的samtools是老版本，我的版本是1.7.

 

gmap使用方法

Consensus sequences, FLNC sequences, and nonredundant transcripts were mapped to the Z. japonica reference transcript sequences (http:// zoysia. kazusa. or. jp) using GMAP [50].
Then, PacBio sequencing was mapped to the bamboo genome using GMAP with the following option: -B 5 -K 8000 -t 40 -f 2 -n 1 (Wu et al., 2016).

安装gmap

在maker安装的时候已经安装好了，可以直接用

1. 建库
   gmap_build -D ./ -d ${S}_genome ${S}_genome.fa

2. 比对
   gmap -B 5 -K 8000 -t 40 -f 2 -n 1 -D ./ -d ${S}_genome $R.transcripts.hq.fasta > $R.transcripts.hq.fasta.gmap 2> $R.transcripts.hq.fasta.fail