NOTE

python

State “TODO” from [2021-12-21 二 16:20]

导入数据包时注意当前目录下是否有同样名称的包, 有的话会默认导入当前目录的

数据分析包numpy pandas 要特别注意 nan　问题

检查问题时先检查程序逻辑，不要检查(或怀疑python)

python 字典update 不会返回值

pip -i 可以指定镜像提高下载速度

python csv.Reader 遇到只有一个”时会跨行解析

python 调用R包rpy学习

./pip install -U -i https://pypi.tuna.tsinghua.edu.cn/simple sklearn

流畅的python通读

数据模型

State “DONE” from “NEXT” [2018-05-06 日 22:22]

数据结构\列表\字典\文本

State “DONE” from “NEXT” [2019-08-12 Mon 09:36]

函数对象

State “NEXT” from “TODO” [2022-02-03 四 16:42]
State “TODO” from [2022-02-03 四 16:42]

State “NEXT” from “DONE” [2020-01-13 Mon 08:59]
State “DONE” from “PROJECT” [2020-01-13 Mon 08:59]
State “PROJECT” from “DONE” [2020-01-13 Mon 08:59]
State “DONE” from “PROJECT” [2020-01-13 Mon 08:59]
State “PROJECT” from “DONE” [2020-01-13 Mon 08:58]
State “DONE” from “PROJECT” [2020-01-13 Mon 08:58]
State “PROJECT” from “DONE” [2020-01-13 Mon 08:58]
State “DONE” from “NEXT” [2020-01-13 Mon 08:58]

NEXT 面向对象

NEXT 控制流程

NEXT 元编程

NEXT 有无快速的debug方法可以考虑用pdb

NEXT 类里调用类外函数时,如何传递变量,不global的情况,用于pool.map 不能使用类函数的时候

提示 tupple object not callable 时检查括号后是否缺少”,”

NEXT 需要学习Makefilell

NEXT 看下python正则表达式的compile

NEXT 学习python yield

NEXT 学习python并发与参数的自动解包

测试接口或其它不要在装有python 包的地方测试

Pandas 默认空值为Nan 浮点型，空字符串问题更少

python 自动完成可以在引号内的的第一个字符就匹配么？

pd.concat 无视索引列名称

strip() strip(“\n”) 前者可以对\r \n \s \t多种有效，用于处理多操作系统文件时有利，但是如果想保留空字符串有些不方便的地方

python 写入excel单元格换行问题？

web input 是会对每个子类都有效么？

subprocess 调用系统命令时有的特数字符可能会造成命令无效

递归函数有默认参数时，后面的不会按默认进行

python 列表中换行用”’ 注释好想无效

data = [ (‘cog_id’, cog_id),

(‘anno_type’, anno_type), (‘type’, line[0]), (‘function_categories’, “[” + line[2] + “]” + ” ” + line[1]), (‘cog’, int(line[3])), ] ”’ (‘function_categories’, line[1]), (‘cog’, int(line[2])), (‘nog’, int(line[3])) ”’

other

cytoscape 导入文件为txt, 不能把其修改为xls结尾的东西

总做流设置out_file时不允许文件不存在，会报错，该错误不可以通过try..except..跳过，这样做仍然会被框架捕获

python多线程， threadingTreading 创建的线程异常退出时不会有影响正常工作流的运行，要注意仔细核查日志的错误

cc1plus: error: unrecognized command line option “-Wpedantic” 升级gcc版本5.10 解决

GitLab: This deploy key does not have write access to this project. fatal: Could not read from remote repository.

Please make sure you have the correct access rights and the repository exists.

~/.ssh/config Host git.majorbio.com

RSAAuthentication yes Identityfile ~/.ssh/dev Host lbx.majorbio.com HostName git.majorbio.com User git IdentityFile ~/.ssh/id_rsa.liubinxu IdentitiesOnly yes

git clone git@git.majorbio.com:liu.binxu/gene_db.git git clone git@lbx.majorbio.com:liu.binxu/gene_db.git 使用指定的key git remote set-url origin git@lbx.majorbio.com:sanger_bioinfo/SangerBiocluster.git

curl socks5 代理 curl –socks5-hostname 127.0.0.1:1080 http://rest.kegg.jp/list/pathway/map -o map

编译项目时出现cc1plus: error: unrecognized command line option “-std=c++11” #254 升级gcc版本解决

rsa”: bad permissions

chmod 600 /etc/ssh/ssh_host_rsa_key /etc/ssh/ssh_host_ecdsa_key /etc/ssh/ssh_host_ed25519_key

重新启动ok systemctl start sshd

疑问：

python 并行是map 调用函数的global 列表不会修改

slurm问题在计算节点机器上运行tool command可以直接运行，投递却不可以，内存设置过小时报段错误，返回码 -11 ，直接投递命令

#SBATCH –mem=4G /var/spool/slurmd/job761474/slurm_script: line 13: 36020 Segmentation fault

再次修改kegg file文件时发现init文件的路径不起效，看了下函数发现函数里重定义了路径，应该是重运行tool时路径从pk文件里重载所以这样修改的

使用基因集时把is_use字段更新, to_file里更新比较合适

et tree 如何去除 svg 中 ns0

add_commond中不允许有；换行, samtools 参数会传递错误,不知道其它命令有没有问题

add_commond需要注意命令返回值, 有的情况下看似h提示了错误,结果也不正确,但返回值是0, 正确的错误会在后续运行中报出

检查逻辑,尤其是在判断语句为逻辑语句时,容易出错

smallrna bowtie流程，不写large-index参数，bowtie无法自动识别长索引

State “DONE” from “NEXT” [2019-05-24 Fri 17:23]

linux 回车指令也会执行一次PROMPT_COMMAND 但不产生history

Warning (initialization): An error occurred while loading ‘/mnt/ilustre/users/sanger-dev/sg-users/liubinxu/work/.emacs.d/init.el’:

error: Required feature ‘init-putty’ was not provided

To ensure normal operation, you should investigate and remove the cause of the error in your initialization file. Start Emacs with the ‘–debug-init’ option to view a complete error backtrace.

git reset 回退使用HEAD^ 时无法指定单文件

python inspect 包可以打印源代码，但是有修饰符时不可以

ssh config 可以指定git 连接时使用的key

~/.config/flake8 调整flake8的warnning数量

V2重运行 ~/wpm2/bin/run_work

excel url 数量不超过65530R

UWSGI NGINX 如何自动重启

mongo elastic search 数据库学习

NEXT 迁移命令行记录过来

mongo 查询方法研究聚合查询

elasticsearch head 概念是什么？ _routing和_parent 内置变量的含义

GET 后跟 json 也会插入GET sg_dev_cmds/cmds/2?version=4 {“aa”: “dss”} API还可以检查 document 是否使用 HEAD termvectors 必须fields GET sg_dev_cmds/cmds/103/_termvectors?fields=cmds 分词 simple 有下划线http://localhost:9200/_analyze?analyzer=standard&pretty=true&text=test测试缺少数字换成编码 https://stackoverflow.com/questions/15501517/elasticsearch-char-filter-replace-any-character-with-whitespace 或者模式分词 https://www.elastic.co/guide/en/elasticsearch/reference/current/analysis-pattern-tokenizer.html https://www.elastic.co/guide/en/elasticsearch/reference/5.6/analysis-edgengram-tokenizer.html

可以通过新设analyzer 实现 https://www.elastic.co/guide/en/elasticsearch/reference/5.6/configuring-analyzers.html

PUT customer_test3 { “settings”: { “analysis”: { “tokenizer”: { “my_tokenizer”: { “type”: “pattern”, “pattern”: “[ _]” } }, “analyzer”: { “default”: { “tokenizer”: “my_tokenizer”, “filter”: [“lowercase”] } } } }, “mappings”: {

} } scroll 搜索时返回的num是总体的num mongo数据提取时 clone.info info被识别为clone的属性，导致clone 的属性不能被插入, 使用以下命令查看自适应属性 GET genedb_project/_mapping “clone” : { “properties” : { “info” : { “type” : “text”, “fields” : { “keyword” : { “type” : “keyword”, “ignore_above” : 256 } } } } },

s3 命令行程序 s3cmd

_type可以作为聚合的字段，列表数据的字段也可以聚合

py bulk 给了type必须给id

“Result window is too large, from + size must be less than or equal to: [10000] but was [10010]. See the scroll api for a more efficient way to request large data sets. This limit can be set by changing the [index.max_result_window] index level setting.”

_id 不可以有重复

softinstall

cpan 安装时可能用到变量LIBRARY_PATH

<<<<<<< HEAD

apache cgi LoadModule cgid_module modules/mod_cgid.so 如果开始就倒入，会将所有文件都执行， script-cgi 指定文件类型无效，必须不倒入启动一次，再倒入启动一次 ScriptAlias修改为 Alias可以解决这个问题

NODE 安装时报以下问题使用”yarn add -D webpack-cli” 命令行解决

[1] [1] > mongo-express@1.0.0-alpha.4 build-dev /mnt/lustre/users/sanger-dev/sg-users/liubinxu/soft/mongo-express [1] > webpack –watch [1] [1] CLI for webpack must be installed. [1] webpack-cli (https://github.com/webpack/webpack-cli) [1] [1] We will use “yarn” to install the CLI via “yarn add -D webpack-cli”. [1] Do you want to install ‘webpack-cli’ (yes/no): [nodemon] 2.0.12 [0] [nodemon] to restart at any time, enter `rs` [0] [nodemon] watching path(s): lib/**/* [0] [nodemon] watching extensions: js,mjs,json [0] [nodemon] starting `node app.js` [0] internal/modules/cjs/loader.js:883 [0] throw err; [0] ^ [0] [0] Error: Cannot find module ‘express-fileupload’ [0] Require stack: [0] - /mnt/lustre/users/sanger-dev/sg-users/liubinxu/soft/mongo-express/lib/middleware.js [0] - /mnt/lustre/users/sanger-dev/sg-users/liubinxu/soft/mongo-express/app.js [0] at Function.Module._resolveFilename (internal/modules/cjs/loader.js:880:15) [0] at Function.Module._load (internal/modules/cjs/loader.js:725:27) [0] at Module.require (internal/modules/cjs/loader.js:952:19) [0] at require (internal/modules/cjs/helpers.js:88:18) [0] at Object.<anonymous> (/mnt/lustre/users/sanger-dev/sg-users/liubinxu/soft/mongo-express/lib/middleware.js:6:20) [0] at Module._compile (internal/modules/cjs/loader.js:1063:30) [0] at Object.Module._extensions..js (internal/modules/cjs/loader.js:1092:10) [0] at Module.load (internal/modules/cjs/loader.js:928:32) [0] at Function.Module._load (internal/modules/cjs/loader.js:769:14) [0] at Module.require (internal/modules/cjs/loader.js:952:19) { [0] code: ‘MODULE_NOT_FOUND’, [0] requireStack: [ [0] ‘/mnt/lustre/users/sanger-dev/sg-users/liubinxu/soft/mongo-express/lib/middleware.js’, [0] ‘/mnt/lustre/users/sanger-dev/sg-users/liubinxu/soft/mongo-express/app.js’ [0] ] [0] } [0] [nodemon] app crashed - waiting for file changes before starting…

conda下无法安装uwsgi https://github.com/conda-forge/uwsgi-feedstock

uwsgi –reload uwsgi.pid 重启uwsgi

=======

./specs: 目录存在需要新建目录在目录下编译

PKG_CONFIG_PATH 必须export才有效

[sanger-dev@login-0-9 pkgconfig]$ export PKG_CONFIG_PATH=”/mnt/lustre/users/sanger-dev/app/library/share/pkgconfig” [sanger-dev@login-0-9 pkgconfig]$ pkg-config –exists xorg-sgml-doctools [sanger-dev@login-0-9 pkgconfig]$ pkg-config –libs “xorg-sgml-doctools”

[sanger-dev@login-0-9 pkgconfig]$ pkg-config –libs “xorg-sgml-doctools >= 1.8”

export ACLOCAL_PATH=/usr/share/aclocal 自动编译缺少m4文件

>>>>>>> 07dcdcfe173b1367ca91c4d482d019cb217249ac

linux安装dingding

sanger 开发研究

蛋白kegg图片错误，发现存在对象存储缓存问题，如果之前维护是修改了对象存储的硬链接，第二次使用该文件时跳过下载单文件已经不存在了

转录因子动物时不能添加表达量表格， meme文件中的id找不到表达量导致相关系数为0 pvalue为1

NEXT sanger file 文件对象事先loginfo

基因集的接口首先判断基因集是否为空

State “DONE” from “NEXT” [2020-04-27 Mon 10:22]

接口传入参数到params ，逻辑修改会造成重运行出错接口传入参数到options，逻辑修改会造成运行出错

开发规范整理：

接口：工作流： module： tool：

wgcna 相关记录不用的字段删除，树状图文件

NEXT 命令行调用tool

多线程为何子线程不会终止 /mnt/ilustre/users/sanger-dev/workspace/20200525/TfPredict_tsg_37303_8774_7767/TfPredict2

mongo api 顺利导出数据到json格式

tools 不可以调用MultiTransfer 的包下载文件在下载后add_download 会自动跳出是为什么没有正确的写end？

tsg 日志查看工具 log_wf_last 查看

流程开发中的默认值应该如何设置

option 后自动加()

Single_workflow 不能运行workflow

none 不可以傳入字符串參數

UWSGI NGINX 学习，常见错误排查 config.d 可以找到配置文件，包含acess 和 error

AGENT 中如果add_upload_dir 重运行会出错，内存错误跑了多次时？

框架中的nr2GO 内存溢出被杀掉，重新投递，如果没有被杀，则会被卡死, slurm 内存管理的问题？

perl pool.map 的运行机制最后一个线程总是切换，内存增加然后被卡死 /mnt/lustre/users/sanger/workspace/20201027/Denovorna_majorbio_293734/AnnotMapdb/Nr2go15__1/nr2go_resource.txt

软件安装培训

State “DONE” from “NEXT” [2018-03-25 日 14:04]

表结构与导表函数培训

转录组组装分享

State “DONE” from “NEXT” [2019-08-30 Fri 11:29]

新人培训ppt

State “DONE” from “NEXT” [2019-07-30 Tue 08:34]

CANCELLED 学习svg试图破解String

State “NEXT” from “DONE” [2020-04-28 Tue 12:40]
State “DONE” from “PROJECT” [2020-04-28 Tue 12:40]
State “PROJECT” from “DONE” [2020-04-28 Tue 12:40]
State “DONE” from “NEXT” [2020-04-28 Tue 12:40]

学习python xmlpackage

State “DONE” from “NEXT” [2018-02-22 四 20:48]

再看下对象存储配置时的name对应关系

wpm服务流程时间过长造成status表无法更新

NEXT 查看工作流参数传递，参数类型如何强制转换

NEXT 为什么修改配置文件需要重启工作流

tryforgood 为什么和下载s3文件冲突

ellipse 置信区间有写入group的步骤如果同时运行多个可能造成 group读取时错

框架存在进程由于阻塞tool被杀的情况？失联又重运行又失联？, 投递脚本被杀, 推测别的module阻塞主进程

工作流不写 super(MitargetWorkflow, self).run() 一段时间后可能流程终止且不会报错

动态库接口测试添加以下行

contract_id=’hsnlsr7847llciep42lupkfps8’, dydb=”1”

生信

部分物种的注释使用masked基因组没有替换 bowtie2的索引， 112上的基因组和hisat2索引也未替换

报错信息应该注意从前往后,有时颜色不显著

ssh socket错误,不影响scp传输文件

原核转录组rockhopper 存在问题，在于输入参考的序列　index顺序, 调整顺序后可能运行出来

kegg　link问题可以尝试在后面同一个边框的Ｋ* 中筛除一部分(比如如果有多个就筛掉单个基因集注释的部分)，　不过也存在分线，如果筛掉的Ｋ*存在与其它边框就会出错

edgeR makeContrasts 输入为表达式时，直接写可以不加contrast 参数，否则必须加

javascript vue html

npm view w3c-xmlhttprequest 查看package版本 git 不能使用https下载修改 json中的git+https 为git

emacs

emacs补全提示框背景和前景都为黑色

解决ipython乱码的问题,新版貌似不太支持,删除了相关函数

State “DONE” from “NEXT” [2018-05-06 日 22:26]

查看putty下emacs为什么shift + 方向键无效

State “DONE” from “NEXT” [2020-01-07 Tue 15:10]

/mnt/ilustre/users/sanger-dev/workspace/20190522/LncRna_tsg_34266/remote_input/qc_dir

用yasnippet写python的模板

写三个file读写相关的

State “DONE” from “NEXT” [2018-05-06 日 22:28]

写log日志相关的

State “DONE” from “NEXT” [2018-05-11 五 21:17]

NEXT 写git文档相关的

CANCELLED emacs加载正确的python package变量以方便定位函数

State “NEXT” from “TODO” [2023-02-15 Wed 08:30]
State “TODO” from [2023-02-15 Wed 08:30]

State “NEXT” from “DONE” [2020-05-18 Mon 08:34]
State “DONE” from “PROJECT” [2020-05-18 Mon 08:34]
State “PROJECT” from “DONE” [2020-05-18 Mon 08:34]
State “DONE” from “PROJECT” [2020-05-18 Mon 08:34]
State “PROJECT” from “DONE” [2020-05-18 Mon 08:34]
State “DONE” from “PROJECT” [2020-05-18 Mon 08:34]
State “PROJECT” from “DONE” [2020-05-18 Mon 08:34]
State “DONE” from “NEXT” [2020-05-18 Mon 08:34]

NEXT emacs 生成工作日志方法

脚本自动添加参数yasnipt options

学习https://www.devalot.com/articles/2008/07/project-planning.html

emacs 调用函数时如何提示函数参数

State “DONE” from “NEXT” [2020-06-02 Tue 13:12]

flycheck mode 下一个错误

?搜索变量定义位置

如何在复杂的括号间跳转

研究下spacemacs的配置

emacs linum 会使速度变慢

emacs flycheck检查python时为什么这么慢？有办法提高, 新版貌似可以

emacs python自动完成未知类型时如何使用

学习ivy grep replace counsel-git-grep M-q 替换

State “DONE” from “NEXT” [2020-07-23 Thu 14:42]

EMACS C-= 快捷键无效, C-. 等几个快捷键无法捕获如何设置？

如何切换语法检查为 python2版

emacs 拼写检查有没有可能换行时添加， jedi自动补全慢, 系统任务多时慢，使用自己电脑

anaconda mode python server下载有问题， easy_install 国内镜像,, 公司居然由于aspell 找不到字典影响了补全

以下错误通常是由于时间触发了多次导致的

Exception: 模块AnnotMergeid(annot_db_all_hsa_medical_test2.RefDbAnnotation.AnnotMergeid), start事件已经启动监听，绑定事件处理函数应该在启动事件前进行!

emacs python 错误提示，不提示变量定义(原因 python 解释器 flychecker python 解释器为python3)

JEDI自动补全慢, 切换服务器补全失效？, 是否可以取消显示definition 的功能

emacs python 自动补全总是失效，重启可以解决，原因不明

emacs LSP mode学习

emacs company 是否会有和 LSP complete 不兼容的现象，目前python的补全任然靠anaconda 需要添加withc参数但是顺序有问题

NEXT Emacs 自动提示错误 Warning (flycheck): Syntax checker python-pylint reported too many errors (801) and is disabled.

emacs wgrep研究

emacs which-key develop分支下回收非develop目录的影响

develop 分支go lsp mode无法自动完成

vscode

学习下vim的快捷键

State “TODO” from “NEXT” [2021-01-03 日 13:41]
State “NEXT” from “STARTED” [2021-01-03 日 13:41]
State “STARTED” from “NEXT” [2021-01-03 日 13:41]
State “NEXT” from “TODO” [2021-01-03 日 13:39]

vscode window 如何同步文件导linux sftp插件学习

State “NEXT” from “TODO” [2022-01-24 一 16:26]
State “TODO” from “NEXT” [2021-01-04 一 13:41]

git

GIT 合并丢失文件问题和合并错误问题, 初步判断为git 合并toollab 0908日导致的，但均为正常操作不知如何导致操作间隔比较小有可能是文件没有修改过来, 分支还在update上

2020-09-08 18:59:53:sanger-dev:/mnt/ilustre/users/sanger-dev/sg-users/liubinxu/work/SangerBiocluster/:git checkout master_20200819 2020-09-08 19:00:06:sanger-dev:/mnt/ilustre/users/sanger-dev/sg-users/liubinxu/work/SangerBiocluster/:git merge tool_lab_rna 2020-09-08 19:00:47:sanger-dev:/mnt/ilustre/users/sanger-dev/sg-users/liubinxu/work/SangerBiocluster/:emacs -nw -Q src/mbio/workflows/ref_rna_v2/refrna.py 2020-09-08 19:00:56:sanger-dev:/mnt/ilustre/users/sanger-dev/sg-users/liubinxu/work/SangerBiocluster/:git checkout – src/mbio/workflows/ref_rna_v2/refrna.py 2020-09-08 19:01:15:sanger-dev:/mnt/ilustre/users/sanger-dev/sg-users/liubinxu/work/SangerBiocluster/:git commit -m “和并 tool_lab” 2020-09-08 19:01:32:sanger-dev:/mnt/ilustre/users/sanger-dev/sg-users/liubinxu/work/SangerBiocluster/:git add src/mbio/workflows/ref_rna_v2/refrna.py 2020-09-08 19:01:43:sanger-dev:/mnt/ilustre/users/sanger-dev/sg-users/liubinxu/work/SangerBiocluster/:git commit -m “和并 tool_lab”** 导表失败Failed to insert records into table sg_exp_detail as: batch op errors occurred

git add .出现尚未暂存以备提交的变更有可能子路径中有仓库 “.git”

go

GO 指南windows安装不成功

Couldn’t find tour files: could not find go-tour content; check $GOROOT and $GOPATH https://learnku.com/go/wikis/38166

go学习示例s3上传 https://github.com/larrabee/s3sync/tree/master/cli

linux

同步脚本根据git仓库的路径判断文件传递地址

emacs自动调用脚本同步修改识别 .git文件为根目录, 用Sanger_biocluster解决

State “DONE” from “NEXT” [2020-05-07 Thu 11:25]

写git 自动填充脚本

linux 命令行快捷键

模仿xtract 写json tract

linux screen C-a 快捷键与linux 冲突, 修改screenrc解决

linux screen less 显示文件错误，环境没有问题 bash init-file 导致的能加载环境变量但是可能已经到了screen里面

crontab 学习

peco 配置文件

强化less , find 速度太慢

State “DONE” from “NEXT” [2020-07-23 Thu 15:15]

NEXT windowsputy终端可以直接导剪切板么

学习xclip xsel 剪贴板， crontab 定时任务, crontab 在unbuntu notify-send无效？

State “OTHERS” from “WAIT” [2021-12-21 二 16:11]
State “STARTED” from “NEXT” [2021-12-21 二 13:11]

crontab 无效，sh 没有用绝对路径？ xsel X 在 putty 加载 bash init 后无效, ssh 到别的节点又无效修改display 变量 No Access Control 的勾勾一定要勾 http://www.uuc.me/1211.html

同步文件到ＶＰＳ

sg_complete 自动补全命令完善

线上配置文件生成

State “DONE” from “NEXT” [2020-05-13 Wed 18:17]

字段添加 user, ip等没有记录

考虑使用c写套接字链接

命令行记录引号会换行

自己安装的python 比系统自带的慢

自动记录可以记录 * 么？

错误记录如LS-RTL 以及误输入的中文也会记录

peco C-f C-e快捷键无效

NEXT 一键去想去的工作流目录能不能自动存入一些目录

引号中的引号转义字符会自动去掉, shell识别后传递到python的, linux read -r参数可以解决

为什么随着时间推移占用cpu会增加

网络传输只能传输一部分

slurm 投递的任务没有部分环境变量如 HOME

{‘TMP’: ‘/mnt/ilustre/users/sanger-dev/workspace/tmp’ ‘HOSTNAME’: ‘s-1-12’ ‘SLURM_NTASKS’: ‘1’ ‘SLURM_SUBMIT_DIR’: ‘/’ ‘SLURM_NODEID’: ‘0’ ‘SLURM_JOBID’: ‘3296688’ ‘ENVIRONMENT’: ‘BATCH’ ‘SLURM_TOPOLOGY_ADDR_PATTERN’: ‘node’ ‘SLURM_JOB_ACCOUNT’: ‘local’ ‘PATH’: ’mnt/ilustre/users/sanger-dev/app/gcc/5.1.0/bin:/mnt/ilustre/users/sanger-dev/app/bioinfo/itraq_and_tmt/libsvm-3.22:/mnt/ilustre/users/sanger-dev/app/bioinfo/itraq_and_tmt/blast-2.2.23/bin/:/mnt/ilustre/users/sanger-dev/app/program/Python/bin:/sbin:/usr/sbin:/bin:/usr/bin’ ‘SLURM_CPUS_PER_TASK’: ‘20’ ‘LD_LIBRARY_PATH’: ‘/mnt/ilustre/users/sanger-dev/app/gcc/5.1.0/lib64:/mnt/ilustre/users/sanger-dev/app/library/lib:/mnt/ilustre/users/sanger-dev/app/library/lib64:/mnt/ilustre/users/sanger-dev/app/program/Python/lib:’ ‘SLURM_JOB_NODELIST’: ‘s-1-12’ ‘SLURM_JOB_USER’: ‘sanger-dev’ ‘LANG’: ‘en_US.UTF-8’ ‘TERM’: ‘dumb’ ‘SLURM_LOCALID’: ‘0’ ‘TEMP’: ‘/mnt/ilustre/users/sanger-dev/workspace/tmp’ ‘SLURM_TASK_PID’: ‘37654’ ‘SHLVL’: ‘5’ ‘SLURM_JOB_QOS’: ‘Added as default’ ‘SLURM_JOB_UID’: ‘1001’ ‘SLURM_NODELIST’: ‘s-1-12’ ‘SLURM_JOB_CPUS_PER_NODE’: ‘20’ ‘TMPDIR’: ‘/mnt/ilustre/users/sanger-dev/workspace/tmp’ ‘SLURM_PROCID’: ‘0’ ‘SLURM_TASKS_PER_NODE’: ‘1’ ‘SLURM_JOB_NUM_NODES’: ‘1’ ‘SLURM_SUBMIT_HOST’: ‘login-0-0.local’ ‘SLURM_NPROCS’: ‘1’ ‘PYTHONPATH’: ‘/mnt/ilustre/users/sanger-dev/biocluster/src:’ ‘SLURM_CLUSTER_NAME’: ‘rocks-cluster’ ‘SLURM_JOB_PARTITION’: ‘SANGER’ ‘SLURM_JOB_ID’: ‘3296688’ ‘SLURM_NODE_ALIASES’: ‘(null)’ ‘SLURM_CPUS_ON_NODE’: ‘20’ ‘SLURM_MEM_PER_NODE’: ‘20480’ ‘SLURM_JOB_GID’: ‘1000’ ‘_’: ‘/mnt/ilustre/users/sanger-dev/app/program/Python/bin/python’ ‘SLURM_PRIO_PROCESS’: ‘0’ ‘SLURM_GTIDS’: ‘0’ ‘PYTHON_EGG_CACHE’: ‘/mnt/ilustre/users/sanger-dev/biocluster/cache’ ‘SLURM_NNODES’: ‘1’ ‘SLURM_JOB_NAME’: ‘Dia.ProteinAnnotation.Multiloc’ ‘SLURM_TOPOLOGY_ADDR’: ‘s-1-12’ ‘PWD’: ‘/mnt/ilustre/users/sanger-dev/workspace/20210108/Dia_tsg_249383/ProteinAnnotation/Multiloc’ ‘SLURM_CHECKPOINT_IMAGE_DIR’: ‘/var/spool/slurm.checkpoint’ ‘SLURMD_NODENAME’: ‘s-1-12’}

python 多线程抛出以下异常往往是线程函数的问题

Traceback (most recent call last): File “/mnt/lustre/users/sanger-dev/wpm2/sanger_bioinfo/src/mbio/packages/ref_genome_db_medical/getid_common.py”, line 95, in <module> tran2id = mapping_id(idmapping_db=idmapping) File “/mnt/lustre/users/sanger-dev/wpm2/sanger_bioinfo/src/mbio/packages/ref_genome_db_medical/getid_common.py”, line 71, in mapping_id for a_acc2id in acc2ids: File “/mnt/lustre/users/sanger-dev/app/program/Python/lib/python2.7/site-packages/concurrent/futures/_base.py”, line 641, in result_iterator yield fs.pop().result() File “/mnt/lustre/users/sanger-dev/app/program/Python/lib/python2.7/site-packages/concurrent/futures/_base.py”, line 455, in result return self.__get_result() File “/mnt/lustre/users/sanger-dev/app/program/Python/lib/python2.7/site-packages/concurrent/futures/_base.py”, line 414, in __get_result

pupeteer 遇到以下问题史slurm内存不足导致

(node:3708) UnhandledPromiseRejectionWarning: Error: Failed to launch the browser process! Fontconfig warning: “/etc/fonts/fonts.conf”, line 86: unknown element “blank” [0224/160451.417909:ERROR:browser_main_loop.cc(530)] Failed to open an X11 connection. [0224/160451.675277:ERROR:platform_thread_posix.cc(147)] pthread_create: Resource temporarily unavailable (11) [0224/160451.676172:ERROR:platform_thread_posix.cc(147)] pthread_create: Resource temporarily unavailable (11) [0224/160451.676695:ERROR:platform_thread_posix.cc(147)] pthread_create: Resource temporarily unavailable (11) [0224/160451.745469:ERROR:platform_thread_posix.cc(147)] pthread_create: Resource temporarily unavailable (11) [0224/160451.769138:ERROR:platform_thread_posix.cc(147)] pthread_create: Resource temporarily unavailable (11) [0224/160451.745922:FATAL:simple_thread.cc(55)] Check failed: success. #0 0x5594e1903f49 base::debug::CollectStackTrace() #1 0x5594e186d933 base::debug::StackTrace::StackTrace() #2 0x5594e1881500 logging::LogMessage::~LogMessage() #3 0x5594e188204e logging::LogMessage::~LogMessage() #4 0x5594e18ee66f base::SimpleThread::StartAsync()

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