sudo apt purge cmake
sudo apt autoremove

Downloading the new

https://cmake.org/files/v3.11/cmake-3.11.1-Linux-x86_64.sh
sudo mkdir /opt/cmake
sudo sh cmake-3.11.1-Linux-x86_64.sh --prefix=/opt/cmake --skip-license

Make it available

sudo update-alternatives --install /usr/bin/cmake cmake /opt/cmake/bin/cmake 1 --force

wget 'https://annoroad-cloud-product.oss-cn-beijing.aliyuncs.com/user/cache/project/XS01KF2023110197/PM-XS01KF2023110197-15/ANNO_XS01KF2023110197_PM-XS01KF2023110197-15_2024-11-15/Cleandata/DNA-ZM3/DNA-ZM3_R1.fq.gz?OSSAccessKeyId=LTAI4G7bDDSRkyJhvK1vsUyE&Expires=1731763573&Signature=W2FD94gWBUQjeni8YSd2Rcgs6YE%3D'

k8s网络

seqkit：序列梳理神器-统计、格式转换、长度筛选、质量值转换、翻译、反向互补、抽样、去重、滑窗、拆分等30项全能

1. 安装

conda install -c bioconda seqkit

2. 功能

amplicon        通过引物检索扩增子(或其周围的特定区域)
bam             检查和在线绘制BAM记录文件的直方图
common          通过id/名称/序列查找多个文件的公共序列
concat          连接多个文件中具有相同ID的序列
convert         转换FASTQ质量编码格式：支持格式包括：桑格，Solexa和Illumina
duplicate       重复序列N次
faidx           创建FASTA索引文件并提取子序列
fish            使用局部比对在较大的序列中寻找短序列
fq2fa           转换FASTQ到FASTA
fx2tab          将FASTA/Q转换为表格格式(包含长度/GC含量/GC偏好)
genautocomplete 生成shell自动完成脚本
grep            通过ID/name/sequence/sequence motif搜索序列，允许错配
head            打印第一条序列
help            打印帮助信息
locate          定位序列，或者motifs，允许错配
mutate          编辑序列(点突变、插入、删除)
pair            匹配双端序列文件
range           打印一个范围内的序列
rename          重命名重复序列ID
replace         使用正则表达式修改名称或者序列
restart         重置环状基因组的起始位置
rmdup           通过id/名称/序列删除重复的序列
sample          按数量或比例对序列进行抽样
sana            清理损坏的单行fastq文件
scat            real time recursive concatenation and streaming of fastx files
seq             转换序列(反向，补充，提取ID…)
shuffle         随机序列
sliding         序列滑窗提取，支持环形基因组
sort            按id/名称/序列/长度排序序列
split           按id/seq区域/大小/部件将序列拆分为文件(主要用于FASTA)
split2          按序列数量/文件数将序列拆分为多个文件(FASTA, PE/SE FASTQ)
stats           FASTA/Q文件的简单统计
subseq          通过region/gtf/bed得到子序列，包括侧翼序列
tab2fx          转换表格格式为FASTA/Q格式
translate       翻译DNA/RNA到蛋白质序列(支持歧义碱基)
version         打印版本信息并检查是否更新
watch           序列特征的监测和在线直方图

参数

Flags:
      --alphabet-guess-seq-length int   seqkit根据第一个FASTA记录猜测序列类型的序列前缀的长度(0表示整个序列)(默认10000)
  -h, --help                            显示帮助
      --id-ncbi                         FASTA头是ncbi风格的，例如>gi|110645304|ref|NC_002516.2 
      --id-regexp string                用于解析ID的正则表达式(default "^(\\S+)\\s?")，匹配空格前的部分为序列名
      --infile-list string              输入文件列表中的文件 (one file per line), if given, they are appended to files from cli arguments
  -w, --line-width int                  输出FASTA格式时的行宽 (0 for no wrap) (default 60)
  -o, --out-file string                 输出 ("-" for stdout, suffix .gz for gzipped out) (default "-") -代表标准输出，加.gz可输出压缩文件
      --quiet                           保持安静，不要显示额外的信息
  -t, --seq-type string                 序列类型 (dna|rna|protein|unlimit|auto) (auto, 按第一个序列自动检测) (default "auto")
  -j, --threads int                     CPU数量 (默认单核为1，多核为2) (default 2)

参考

https://bioinf.shenwei.me/seqkit/
https://mp.weixin.qq.com/s/OJsxFR33ej0ACozNbF_dNA

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Start Share and Storage Management.

In the Share and Storage Management console, in the details pane, click the Shares tab, and then click <share_name> (where share_name is the name of the NFS share).

In the Actions pane, click Properties.

The <share_name> Properties dialog box displays.

In the <share_name> Properties dialog box, on the NFS Authentication tab, select the Enable unmapped user access check box.

On the NFS Authentication tab, click Allow unmapped UNIX user access, and then click OK.

Close the Share and Storage Management console.

https://access.redhat.com/solutions/2316#:~:text=On Linux or Unix systems,to occupy space on disk.

2.编译程序debug 版本 加上-g -O0 一般在项目的Makefile 中

3.gdb 运行程序

gdb --args kmer2read_distr --seqid2taxid $DATABASE/seqid2taxid.map --taxonomy $DATABASE/taxonomy/ --kraken $DATABASE/database.kraken --output $DATABASE/database${READ_LEN}mers.kraken -k ${KMER_LEN} -l ${READ_LEN} -t ${THREADS}

/usr/bin/google-chrome-stable

第2步.创建一个google-chrome.desktop的文件

gedit ~/.local/share/applications/google-chrome.desktop

第3步 修改文件

vi ~/.local/share/applications/google-chrome.desktop
Exec=/usr/bin/google-chrome-stable %u

Jul 26 09:33:25 anneng01 sshd[6536]: error: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
Jul 26 09:33:25 anneng01 sshd[6536]: error: @         WARNING: UNPROTECTED PRIVATE KEY FILE!          @
Jul 26 09:33:25 anneng01 sshd[6536]: error: @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
Jul 26 09:33:25 anneng01 sshd[6536]: error: Permissions 0755 for '/etc/ssh/ssh_host_ed25519_key' are too open.
Jul 26 09:33:25 anneng01 sshd[6536]: error: It is required that your private key files are NOT accessible by others.
Jul 26 09:33:25 anneng01 sshd[6536]: error: This private key will be ignored.
Jul 26 09:33:25 anneng01 sshd[6536]: error: key_load_private: bad permissions
Jul 26 09:33:25 anneng01 sshd[6536]: error: Could not load host key: /etc/ssh/ssh_host_ed25519_key
Jul 26 09:33:25 anneng01 sshd[6536]: fatal: No supported key exchange algorithms [preauth]

后台进入服务器

sudo chmod -R 600 /etc/ssh/
systemctl restart sshd

Failed to allocate directory watch: Too many open files

解决方案：

 sudo vi /etc/sysctl.conf

文件添加：

fs.inotify.max_user_instances=51200

保存成功后：

sudo sysctl -p

将文件生效 重新启动nginx

sudo service  nginx restart

server {
   listen       8022;
   server_name  _;
   root /path/path;
   index index.html;
   location / {
     index index.html index.htm;
     try_files $uri $uri/ @fallback;                                                                       
   }
   location @fallback {
     rewrite ^.*$ /index.html break;
   }
 }

1. Overview
   As we know, we can redirect the standard output (stdout) of a command to a file using the “>” operator in the Linux command line.

However, sometimes, we want to redirect to a file where we don’t have permission to write — for example, “sudo command > file_requires_root_permission“.

In this case, we may get a “Permission denied” error even if we’ve used the sudo command.

In this quick tutorial, we’ll analyze the cause of this problem and address the right ways to solve it.

2. Introduction to the Problem
   An example is probably the best way to explain the problem.

Let’s say we have an empty, plain text file:

kent$ ls -l /opt/output.txt
-rw-r--r-- 1 root root 0 May 8 10:43 /opt/output.txt
The ls output above shows that only user root can write to the /opt/output.txt file.

Now, we attempt to redirect the output of an echo command to the mentioned file as the regular user kent:

kent$ echo "Linux is awesome!" > /opt/output.txt
bash: /opt/output.txt: Permission denied
We’ve gotten the “Permission denied” error. It isn’t hard to understand. This is because we execute the echo command and redirect the output as the kent user, but the user kent has no write permission on the file /opt/output.txt.

We know if we execute a command with sudo, the command will be executed as the root user. Let’s say the user kent has been granted the sudo privilege.

Next, let’s see if we can redirect the echo output to our target file using sudo:

kent$ sudo echo "Linux is awesome!" > /opt/output.txt
[sudo] password for kent:
bash: /opt/output.txt: Permission denied
Oops, after we give the password, we keep having the same error message.

We may ask why we still don’t have permission to write to the file though we’ve used the sudo command?

Next, let’s find the answer to the question.

3. Why Do We Have the “Permission denied” Error?
   To answer the question, let’s take a closer look at the whole echo command. The command has two parts:

The command part: sudo echo “Linux is awesome!”
The redirection part: > /opt/output.txt
The sudo command allows us to execute the echo command as the root user. However, when we write “sudo command > file“, the sudo command won’t affect the redirection part.

In other words, the redirection is still performed as the regular user kent. Therefore, we encounter the “Permission denied” error.

Now that we understand the cause of the problem, let’s discuss the solutions.

We’ll address several different approaches to solve the problem:

Launching a “root” shell to execute the command
Wrapping the command in a shell script
Changing the redirection part into a command
Next, let’s look at these three approaches one by one.

4. Launching a “root” Shell to Execute the Command
   If we can start a shell logged in as the root user and execute our command in this shell, the redirection will also be done by root.

We can pass the -s option to the sudo command to have a “root” shell:

kent$ sudo -s
[sudo] password for kent:
[root]# echo "Linux is awesome!" > /opt/output.txt
[root]# exit
kent$ cat /opt/output.txt
Linux is awesome!
As the output above shows, after executing sudo -s, we’re in an interactive shell with the root user. Then, we can execute the whole command and redirection as root.

The output has also been successfully written to the target file.

5. Wrapping the Command in a Shell Script
   If we can turn the command and redirection into a single command, we can execute it with sudo so that the redirection gets done by root.

Following this idea, we can create a simple shell script file containing our echo command:

kent$ cat myScript.sh
#!/bin/bash
echo "Linux is awesome! - (shell script)" > /opt/output.txt
Next, let’s empty the /opt/output.txt file and test our myScript.sh:

kent$ sudo ./myScript.sh
[sudo] password for kent:
kent$ cat /opt/output.txt
Linux is awesome! - (shell script)
Our shell script works as we expected.

However, it can be inconvenient if we always have to create shell script files for commands with redirections.

If we want to execute such a command only once quickly, we can use sudo bash -c “Command > file” to execute the command with redirection in a sub-shell so that the root user performs both the command and the redirection:

kent$ sudo bash -c 'echo "Linux is awesome! - (sub-shell)" > /opt/output.txt'
[sudo] password for kent:
kent$ cat /opt/output.txt
Linux is awesome! - (sub-shell)
6. Changing the Redirection Into a Command
We’ve learned from a previous section that the sudo command won’t affect the redirection part. However, if we can change the redirection into a command, we can execute it with sudo once again.

The tee command is exactly what we are looking for. tee allows us to redirect the input to a file and stdout. Further, we can launch “sudo tee …” to cause the tee command to be executed as the root user.

Next, let’s test this approach with our example:

kent$ sudo echo "Linux is awesome! - (using tee)" | sudo tee /opt/output.txt >/dev/null
[sudo] password for kent:
kent$ cat /opt/output.txt
Linux is awesome! - (using tee)
As the example above shows, we’ve written the expected value in the /opt/output.txt file.

Since we don’t want to print the text in stdout, we redirect tee‘s stdout to /dev/null.

7. Conclusion
   When we execute commands like “sudo command > file_requires_root“, we may encounter the “Permission denied” error.

In this article, we’ve discussed this error, why it occurs, and several ways to solve the redirection problem.

可以diff检查下

在webpack打包的时候，可以在js文件中混用require和export。但是不能混用import 以及module.exports。
因为webpack 2中不允许混用import和module.exports,
根据线索更改报错
将：

module.exports={***}

改为：

export default {***};

本次GenoStack项目中如何解决：
1、原因在更新WDL版本之前一切正常（目标定位仅是WDL相关代码）
2、然后在WDL依赖相关代码中排查出现module.exports的地方结果有一处确实有出现
3、然后将出现module.exports更改为export default
4、重新打包，发布版本 问题解决