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#+TAGS: { @Office(o) @Home(h) @Call(c) @Way(w) @Lunchtime(l) @GYM(g) @Other(x)}
#+TAGS:
* Projects
** 有参转录组云平台维护和bug修复
*** DONE 数据库 注释查询查不到pathway
SCHEDULED: <2017-10-26 Thu>
*** DONE 跟新小鼠数据库
CLOSED: [2017-12-24 日 20:46]
:LOGBOOK:
- State "DONE" from "" [2017-12-24 日 20:46]
:END:
*** DONE NR数据库描述不正确
CLOSED: [2017-12-24 日 20:46]
:LOGBOOK:
- State "DONE" from "" [2017-12-24 日 20:46]
:END:
*** DONE 重新导入小鼠数据库的表格
CLOSED: [2017-12-24 日 20:46]
:LOGBOOK:
- State "DONE" from "" [2017-12-24 日 20:46]
:END:
*** DONE 注释导表允许空表
CLOSED: [2017-12-26 二 22:17] SCHEDULED: <2017-12-25 日>
:LOGBOOK:
- State "DONE" from "NEXT" [2017-12-26 二 22:17]
:END:
*** DONE 修改导表函数 kegg K 和描述不对应问题
api/database/ref_rna/ref_annotation.py
*** DONE 写一个注释单独导表函数
CLOSED: [2017-12-26 二 22:21]
:LOGBOOK:
- State "DONE" from "NEXT" [2017-12-26 二 22:21]
:END:
*** DONE 设计分片方案，发给郭权
*** DONE 根据要求做对应的修改
CLOSED: [2017-12-27 三 22:29]
:LOGBOOK:
- State "DONE" from "NEXT" [2017-12-27 三 22:29]
:END:
*** DONE 云平台数据库导表，读表结构修改
SCHEDULED: <2017-10-26 Thu>
**** 修改biocluster配置文件
**** 修改app database
**** 修改mbio api web ref_rna文件
**** 修改mbio api to_file文件
**** 修改webroot models mongo文件
**** DONE 接口修改 添加check参数
*** DONE 添加KEGG字段，需跟进下次数据运行结果
CLOSED: [2019-06-21 Fri 17:24]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-06-21 Fri 17:24]
:END:
*** DONE 基因组gtf可能存在有CDS没有对应转录本的情况需要添加，在整理基因组时解决
CLOSED: [2018-02-12 一 22:42]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-02-12 一 22:42]
:END:
*** DONE 参考基因组结尾不是.fa或.fasta时 gatk tools里picard无法识别，annovo也存在同样的问题 在tools/module里进行了修改
CLOSED: [2018-02-12 一 22:43]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-02-12 一 22:43]
:END:
*** DONE 协助安装meme
CLOSED: [2018-05-07 一 19:20]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-05-07 一 19:20]
:END:
google还是比其他的搜索引擎好用, 首先要使使用官方推荐的安装流程,不要一次调整过多参数
遇到的问题是libxml libxslt 有依赖关系而前者往往在服务器上已安装了其它的不对应版本
*** DONE 协助修改启动子序列提取的perl脚本
CLOSED: [2018-05-08 二 22:17]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-05-08 二 22:17]
:END:
*** DONE 注释模块优化
CLOSED: [2019-01-26 六 16:13]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-01-26 六 16:13]
:END:
**** DONE ensemble数据下载流程,暂时告一段落,接下来做注释
CLOSED: [2018-05-08 二 22:18]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-05-08 二 22:18]
:END:
**** DONE 注释比对模块的module编写,go注释流程修改
CLOSED: [2018-05-09 三 19:39]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-05-09 三 19:39]
:END:
**** DONE 修改go 分割处blast2go tools
CLOSED: [2018-05-10 四 21:14]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-05-10 四 21:14]
:END:
**** DONE 测试blast比对模块
CLOSED: [2018-05-11 五 21:16]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-05-11 五 21:16]
:END:
**** DONE nr库diamond获取方式改为本地文件获取
CLOSED: [2018-05-14 一 19:45]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-05-14 一 19:45]
:END:
**** DONE 注释比对流程module测试修改
CLOSED: [2018-05-14 一 19:45]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-05-14 一 19:45]
:END:
module 里的on on rely函数变量一定要写为函数名不可以是函数本身(带括号),应为这样会直接运行
*** DONE rmat安装
CLOSED: [2018-05-07 一 19:23]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-05-07 一 19:23]
:END:
gfortran也可以-fpic
*** DONE 导表优化,修改了blast, swissprot insert_one为insert_many
CLOSED: [2018-06-27 三 18:36]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-06-27 三 18:36]
:END:
*** DONE 注释/分类/富集增加html
CLOSED: [2018-06-07 四 18:10]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-06-07 四 18:10]
:END:
*** DONE KEGG注释模块没有考虑注释结果的可变性(有无新基因注释造成的不同), kgml, png升级造成的不一致 产生了两个bug
CLOSED: [2018-07-30 一 19:21]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-07-30 一 19:21]
:END:
*** DONE 蛋白互做网络
CLOSED: [2018-06-27 三 18:36]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-06-27 三 18:36]
:END:
需写文档
*** DONE 组装模块优化
CLOSED: [2018-06-07 四 18:10]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-06-07 四 18:10]
:END:
*** DONE IPATH
CLOSED: [2018-07-30 一 19:22]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-07-30 一 19:22]
:END:
需要写文档
*** DONE 有参云平台会议,讨论相关原型
CLOSED: [2018-05-11 五 21:15]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-05-11 五 21:15]
:END:
*** DONE 弦图优化添加参数
CLOSED: [2018-06-13 三 18:39]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-06-13 三 18:39]
:END:
需补充开发文档
*** DONE 又遇到了 parafly的错误ignore, 需要改彻底,否则检查错误也很浪费时间
CLOSED: [2019-01-26 六 16:34]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-01-26 六 16:34]
:END:
*** NEXT 参考数据库优化
*** NEXT 优化导表速度
*** NEXT diamond/blast注释可以添加 筛选参数, 根据percent hsp/hit hsp/query 删除predicted字段的比对结果参考github
*** DONE 写ensemble自动下载数据脚本
CLOSED: [2019-06-21 Fri 17:30]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-06-21 Fri 17:30]
:END:
部分物种有子分类目录不能解析
*** NEXT 蛋白互做注意下载的string数据库有可能与官网页面显示的不一致, ID可能幼虫富
*** NEXT 注释流程改为sqlite搜索
*** DONE 有参v1板优化 ,添加蛋白互做, 添加ipath
CLOSED: [2019-01-26 六 16:34]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-01-26 六 16:34]
:END:
表结构有所改动, 注释的origin latest不用传, gene转录本的type 为gene transcript 不是 G T,
**** DONE 已和朱凤娟对接
CLOSED: [2020-05-06 Wed 08:47]
:LOGBOOK:
- State "DONE" from "NEXT" [2020-05-06 Wed 08:47]
:END:
*** DONE ppi 没有过率逼到多个string id的基因,蛋白之前遇到过
CLOSED: [2019-07-24 Wed 15:27]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-07-24 Wed 15:27]
:END:
*** DONE WGCNA lncrna的修改重新同步过来
CLOSED: [2019-07-24 Wed 15:27]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-07-24 Wed 15:27]
:END:
**** TODO 基因数量少时所有基因划到同一个模块 /mnt/lustre/users/sanger/workspace/20190424/WgcnaPipeline_i-sanger_148756_5081_4279
/mnt/lustre/users/sanger/workspace/20190510/WgcnaPipeline_i-sanger_122905_1489_4790/WgcnaModule
**** DONE 样本名重复报错
CLOSED: [2019-06-27 Thu 09:04]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-06-27 Thu 09:04]
:END:
**** DONE 表型数据不可以一列的值完全相等
CLOSED: [2019-06-27 Thu 08:34]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-06-27 Thu 08:34]
:END:
**** DONE 上传数据末尾或开头不可有空格
CLOSED: [2019-06-27 Thu 08:34]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-06-27 Thu 08:34]
:END:
**** DONE R readtable 遇到# 开头的行会忽略掉
CLOSED: [2019-06-27 Thu 08:34]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-06-27 Thu 08:34]
:END:
**** DONE pandas fillna 如果是pad 模式会按照第一个的值向后填充，但第一行不可以有Nan
CLOSED: [2019-06-27 Thu 08:34]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-06-27 Thu 08:34]
:END:
**** DONE kegg问题，基因集注释和富集不对应，没有按数据库过滤
CLOSED: [2019-07-07 Sun 14:46]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-07-07 Sun 14:46]
:END:
**** TODO 富集颜色问题接口差异，需要查看lnc的项目
**** DONE 富集link问题按富集的来的应该按照注释的来，需要查看lnc的项目
CLOSED: [2019-07-07 Sun 14:46]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-07-07 Sun 14:46]
:END:
*** DONE 有参注释逻辑修改
CLOSED: [2019-07-01 Mon 10:29]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-07-01 Mon 10:29]
:END:
*** DONE 有参注释添加表达基因数量统计
CLOSED: [2019-06-10 Mon 19:42]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-06-10 Mon 19:42]
:END:
*** DONE 跟进工作流状况 http://www.tsg.com/Task/index/page_size/10/p/2/page_size/10.html
CLOSED: [2019-07-26 Fri 08:24]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-07-26 Fri 08:24]
:END:
*** DONE 运行新项目
CLOSED: [2019-05-31 Fri 12:58]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-05-31 Fri 12:58]
:END:
*** DONE 运行苏文瑾的所有的转录因子靶基因
CLOSED: [2019-05-30 Thu 10:19]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-05-30 Thu 10:19]
:END:
*** DONE GSEA研发
CLOSED: [2019-07-15 Mon 08:49]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-07-15 Mon 08:49]
:END:
**** DONE GSEA测试pre rank
CLOSED: [2019-06-06 Thu 18:28]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-06-06 Thu 18:28]
:END:
**** DONE gsea 使用基因集会经常不出结果
CLOSED: [2019-06-16 Sun 17:35]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-06-16 Sun 17:35]
:END:
**** NEXT 没有基因name的应该删除还是保留
:LOGBOOK:
- State "NEXT" from "DONE" [2019-06-14 Fri 09:46]
- State "DONE" from "PROJECT" [2019-06-14 Fri 09:46]
- State "PROJECT" from "DONE" [2019-06-14 Fri 09:46]
- State "DONE" from "PROJECT" [2019-06-14 Fri 09:46]
- State "PROJECT" from "DONE" [2019-06-14 Fri 09:46]
- State "DONE" from "NEXT" [2019-06-14 Fri 09:46]
:END:
**** DONE 有参接口流程调通
CLOSED: [2019-06-14 Fri 09:47]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-06-14 Fri 09:47]
:END:
**** DONE 数据库根新
CLOSED: [2019-07-23 Tue 08:38]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-07-23 Tue 08:38]
:END:
**** TODO 看一下gsea是如何校正pvalue的
****
*** DONE bug修复
CLOSED: [2019-07-15 Mon 08:49]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-07-15 Mon 08:49]
:END:
kegg link 颜色错误的问题，lnc项目也应该有
注释不过已知的还是新的用了所有表达的作为背景
*** DONE 有参云平台测试与bug修改
CLOSED: [2020-04-26 Sun 08:47]
:LOGBOOK:
- State "DONE" from "NEXT" [2020-04-26 Sun 08:47]
:END:
*** DONE 整理有参转录组分析说明书
CLOSED: [2020-04-26 Sun 08:47]
:LOGBOOK:
- State "DONE" from "NEXT" [2020-04-26 Sun 08:47]
:END:
*** DONE 高级分级结果目录修改
CLOSED: [2019-07-24 Wed 10:02]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-07-24 Wed 10:02]
:END:
NOTE 已经有error code的无法修改结果目录名需要添加一个没有errorcode的说明记录
*** DONE WGCNA related 空列报错
CLOSED: [2019-07-24 Wed 10:03]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-07-24 Wed 10:03]
:END:
*** DONE 整理开发文档
CLOSED: [2019-07-24 Wed 10:03]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-07-24 Wed 10:03]
:END:
*** DONE 上线
CLOSED: [2019-07-24 Wed 10:03]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-07-24 Wed 10:03]
:END:
**** 软件安装
**** DONE mongo库同步
CLOSED: [2019-07-23 Tue 08:41]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-07-23 Tue 08:41]
:END:
**** DONE 数据库同步
CLOSED: [2019-07-23 Tue 08:41]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-07-23 Tue 08:41]
:END:
*** kegg颜色数据修改统一
*** 差异重运行添加fc值
*** DONE 有参的问题, ppi超出内存 小麦单独设内存
CLOSED: [2020-03-09 Mon 08:58]
:LOGBOOK:
- State "DONE" from "NEXT" [2020-03-09 Mon 08:58]
:END:
SCHEDULED:
*** DONE
*** DONE 查看蛋白kegg的结果统计数量与html标记数量不一致的问题， 原因是注释的数据库使用的是旧版的，html使用新版的
CLOSED: [2020-01-07 Tue 15:12]
:LOGBOOK:
- State "DONE" from "NEXT" [2020-01-07 Tue 15:12]
- State "NEXT" from "DONE" [2019-06-13 Thu 08:39]
- State "DONE" from "NEXT" [2019-06-13 Thu 08:38]
:END:
kegg link链接不到相关的基因ID单物种
/mnt/lustre/users/sanger/workspace/20190606/ProteinsetKegg_sanger_149684_3202_9655
https://report.i-sanger.com/itraq/proteinsetkegg_pathway/task_id/sanger_149684/params/eyJwYXRod2F5X2hyZWYiOiJzM25iOi8vY29tbW9uYnVja2V0L2ZpbGVzL3BhdGh3YXlfaW1nL2l0cmFxL21hcDA0MDEwLnBuZyIsImtlZ2dfaWQiOiI1Y2ZmNTBmMWVkY2IyNTAzY2U5ODZlYmYiLCJuYW1lIjoiUHJvdGVpbnNldEtlZ2dDbGFzc18yMDE5MDYxMV8xNDU3NTM2ODkiLCJ0eXBlIjoiIiAsICJwYXRod2F5X2lkIjoic3NjMDQwMTAifQ==.html
*** NEXT 基因集导表kegg统计 有错误0604已修改
:LOGBOOK:
- State "NEXT" from "DONE" [2019-06-28 Fri 16:01]
- State "DONE" from "NEXT" [2019-06-28 Fri 16:01]
:END:
*** go_DAG： 文件 图形箭头方向错误
*** DONE 沟通弦图筛选基因问题
CLOSED: [2020-05-09 Sat 08:25] SCHEDULED: <2020-05-07 Thu>
:LOGBOOK:
- State "DONE" from "NEXT" [2020-05-09 Sat 08:25]
:END:
*** DONE gsea svg 转pdf失败
CLOSED: [2020-05-07 Thu 17:58] SCHEDULED: <2020-05-07 Thu>
:LOGBOOK:
- State "DONE" from "NEXT" [2020-05-07 Thu 17:58]
:END:
报错在multiprocessing pool 中报
*** DONE kegg 颜色改为蓝色
CLOSED: [2020-05-09 Sat 18:26] SCHEDULED: <2020-05-09 Sat>
:LOGBOOK:
- State "DONE" from "NEXT" [2020-05-09 Sat 18:26]
:END:
*** DONE kegg 数据库修改测试交互
CLOSED: [2020-05-13 Wed 14:26] SCHEDULED: <2020-05-11 Mon>
:LOGBOOK:
- State "DONE" from "NEXT" [2020-05-13 Wed 14:26]
:END:
*** DONE gsea 提取GO 描述信息
CLOSED: [2020-05-09 Sat 08:25]
:LOGBOOK:
- State "DONE" from "NEXT" [2020-05-09 Sat 08:25]
:END:
*** 有参优化文档
*** 注释数据库维护
*** DONE 蛋白单物种图片同步线上和对象存储
CLOSED: [2020-12-29 Tue 08:28] SCHEDULED: <2020-11-30 Mon>
:LOGBOOK:
- State "DONE" from "NEXT" [2020-12-29 Tue 08:28]
:END:
*** DONE 蛋白nr注释， 描述删除多于的内容
CLOSED: [2020-12-03 Thu 16:05] SCHEDULED: <2020-12-02 Wed>
:LOGBOOK:
- State "DONE" from "NEXT" [2020-12-03 Thu 16:05]
:END:
*
*** go_DAG： 文件 图形箭头方向错误
*** DONE 沟通弦图筛选基因问题
CLOSED: [2020-05-09 Sat 08:25] SCHEDULED: <2020-05-07 Thu>
:LOGBOOK:
- State "DONE" from "NEXT" [2020-05-09 Sat 08:25]
:END:
*** DONE gsea svg 转pdf失败
CLOSED: [2020-05-07 Thu 17:58] SCHEDULED: <2020-05-07 Thu>
:LOGBOOK:
- State "DONE" from "NEXT" [2020-05-07 Thu 17:58]
:END:
报错在multiprocessing pool 中报
*** DONE kegg 颜色改为蓝色
CLOSED: [2020-05-09 Sat 18:26] SCHEDULED: <2020-05-09 Sat>
:LOGBOOK:
- State "DONE" from "NEXT" [2020-05-09 Sat 18:26]
:END:
*** DONE kegg 数据库修改测试交互
CLOSED: [2020-05-13 Wed 14:26] SCHEDULED: <2020-05-11 Mon>
:LOGBOOK:
- State "DONE" from "NEXT" [2020-05-13 Wed 14:26]
:END:
*** DONE gsea 提取GO 描述信息
CLOSED: [2020-05-09 Sat 08:25]
:LOGBOOK:
- State "DONE" from "NEXT" [2020-05-09 Sat 08:25]
:END:
*** 有参优化文档
*** 注释数据库维护
*** DONE 蛋白单物种图片同步线上和对象存储
CLOSED: [2020-12-29 Tue 08:28] SCHEDULED: <2020-11-30 Mon>
:LOGBOOK:
- State "DONE" from "NEXT" [2020-12-29 Tue 08:28]
:END:
*** DONE 蛋白nr注释， 描述删除多于的内容
CLOSED: [2020-12-03 Thu 16:05] SCHEDULED: <2020-12-02 Wed>
:LOGBOOK:
- State "DONE" from "NEXT" [2020-12-03 Thu 16:05]
:END:
*** 差异分析edger出的差异不够， pvalue值不够低？导致padjust没有满足条件？, 修改edger 的检验方法可以解决
*** DONE 数据库升级整体方案
CLOSED: [2019-12-23 Mon 08:36]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-12-23 Mon 08:36]
:END:
*** DONE go 分类如果没有结果不要报错
CLOSED: [2020-01-02 Thu 09:07]
:LOGBOOK:
- State "DONE" from "NEXT" [2020-01-02 Thu 09:07]
:END:
*** 注释相关信息下载
**** wiki描述信息下载
**** uniprot描述
**** go描述（官网）
**** 数据整理，插入数据库，mongo. elasticsearch
*** 调控相关信息下载
**** string 蛋白互作
**** smallRNA 调控
**** 转录因子调控
**** biogrid 调控
*** DONE 搜索内容导入
CLOSED: [2021-05-07 Fri 13:40] SCHEDULED: <2021-03-11 Thu>
:LOGBOOK:
- State "DONE" from "NEXT" [2021-05-07 Fri 13:40]
:END:
**** elasticsearch 相关内容研究
*** 研究alliance genome的数据处理流程
*** DONE 学习edirect提取数据方法, eutil编程
CLOSED: [2020-05-15 Fri 14:53] SCHEDULED: <2020-05-14 Thu>
:LOGBOOK:
- State "DONE" from "NEXT" [2020-05-15 Fri 14:53]
:END:
** 有参转录组参考基因组制作
*** DONE 棉花JGI参考基因组整理
SCHEDULED: <2017-10-25 Wed>
注释
核对结果
tsanger注释
核对结果
*** DONE 玉米Annotation文件整理
*** DONE 写做数据库流程
*** DONE NCBI数据库流程 测试
CLOSED: [2018-01-18 四 21:32]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-18 四 21:32]
- State "NEXT" from "DONE" [2018-01-18 四 21:32]
- State "DONE" from "CANCELLED" [2018-01-18 四 21:32]
- State "DELEGATED" from "WAITING" [2018-01-18 四 21:31]
:END:
*** DONE 棉铃虫参考基因组整理
CLOSED: [2017-11-12 Sun 10:37]
:LOGBOOK:
- State "DONE" from "TODO" [2017-11-12 Sun 10:37]
:END:
*** DONE https://www.ncbi.nlm.nih.gov/genome/?term=Punica+granatum 基因组整理
CLOSED: [2017-12-27 三 22:29]
:LOGBOOK:
- State "DONE" from "NEXT" [2017-12-27 三 22:29]
:END:
*** DONE 辣椒参考基因组准备。杜和山给出的
CLOSED: [2017-12-27 三 22:29]
:LOGBOOK:
- State "DONE" from "NEXT" [2017-12-27 三 22:29]
:END:
*** DONE 崔艳艳给的参考基因组整理
CLOSED: [2017-12-27 三 22:29]
:LOGBOOK:
- State "DONE" from "NEXT" [2017-12-27 三 22:29]
:END:
*** DONE bug
**** 数据库KO问题 查询页转录本导表有问题
TestRef数据库任然可能有问题
kegg通路不对应
查询页GO需要重导入
*** DONE 检查各数据库统计结果是否一致
*** DONE 基因组json文件完整性与路径检查
*** DONE 写脚本检查数据库统计不对应问题
*** DONE 查看GO参考导表是否有误
SCHEDULED: <2017-10-27 Fri>
*** DONE 评估崔艳艳参考基因组
SCHEDULED: <2017-11-01 Wed>
*** DONE 核对水稻和草鱼注释结果统计数据量
CLOSED: [2017-11-12 Sun 11:30]
:LOGBOOK:
- State "DONE" from "TODO" [2017-11-12 Sun 11:30]
:END:
*** DONE 烟草2017新版基因组整理
CLOSED: [2017-12-24 日 20:51]
:LOGBOOK:
- State "DONE" from "NEXT" [2017-12-24 日 20:51]
- State "TODO" from "DONE" [2017-11-12 Sun 11:31]
- State "DONE" from "TODO" [2017-11-12 Sun 11:30]
:END:
*** DONE 基因组注释整理COG没有考虑一个基因有多个COG的情况
CLOSED: [2017-12-24 日 20:51]
:LOGBOOK:
- State "DONE" from "NEXT" [2017-12-24 日 20:51]
:END:
*** DONE 刘旋给的两个基因组上线注意type ENSEMBLE正确区分1、2、3
CLOSED: [2017-12-27 三 22:30] DEADLINE: <2017-12-25 一> SCHEDULED: <2017-12-25 一>
:LOGBOOK:
- State "DONE" from "NEXT" [2017-12-27 三 22:30]
:END:
注意type ENSEMBLE正确区分1、2、3
*** DONE 整理辣椒基因组
CLOSED: [2017-12-24 日 20:46]
:LOGBOOK:
- State "DONE" from "TODO" [2017-12-24 日 20:46]
:END:
*** 基因组问题修复
**** DONE 猫基因组问题 使用了rm的版本
CLOSED: [2018-01-04 四 22:24]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-04 四 22:24]
:END:
**** DONE 石榴基因组忘记添加
CLOSED: [2018-01-04 四 22:25]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-04 四 22:25]
:END:
**** DONE 本氏烟基因组忘记添加
CLOSED: [2018-01-05 五 19:01] SCHEDULED: <2018-01-05 五>
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-05 五 19:01]
:END:
**** DONE 真菌基因组问题 使用masked基因组
CLOSED: [2018-01-05 五 19:01]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-05 五 19:01]
:END:
*** DONE 猫的基因组问题
CLOSED: [2018-01-03 三 21:45]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-03 三 21:45]
:END:
cufflink stringtie 组装后边界超出是因为基因组使用了masked缘故
*** DONE 牵牛基因组去除gene: transcript: ensemble下载GFF的问题以后注意使用gtf
CLOSED: [2018-01-26 五 20:29]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-26 五 20:29]
:END:
*** DONE 参考基因组香菇制作刘璇给的新基因组通知彩萍于涵
CLOSED: [2018-02-01 四 20:09] SCHEDULED: <2018-01-29 一> DEADLINE: <2018-01-13 六>
:LOGBOOK:
- State "DONE" from "NEXT" [2018-02-01 四 20:09]
:END:
*** DONE 写一个自动下载整理ensemble基因组的脚本
CLOSED: [2018-07-25 三 19:08] SCHEDULED: <2018-01-29 一>
:LOGBOOK:
- State "DONE" from "NEXT" [2018-07-25 三 19:08]
:END:
*** DONE 注释添加annot_class模块
CLOSED: [2019-06-21 Fri 17:24]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-06-21 Fri 17:24]
:END:
*** DONE 刘璇给的两个基因组整理
CLOSED: [2018-02-01 四 20:09] SCHEDULED: <2018-01-29 一>
:LOGBOOK:
- State "DONE" from "NEXT" [2018-02-01 四 20:09]
:END:
*** DONE 西瓜基因组整理
CLOSED: [2018-02-01 四 20:09] SCHEDULED: <2018-01-29 一>
:LOGBOOK:
- State "DONE" from "NEXT" [2018-02-01 四 20:09]
:END:
*** DONE 刘璇新给的两个基因组
CLOSED: [2018-02-08 四 18:46]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-02-08 四 18:46]
:END:
*** DONE 刘璇给的最后一个基因组交给于涵
CLOSED: [2018-03-06 二 20:07] SCHEDULED: <2018-02-23 五>
:LOGBOOK:
- State "DONE" from "NEXT" [2018-03-06 二 20:07]
:END:
*** DONE 基因组不可以使用masked建的索引需要重建
CLOSED: [2018-03-06 二 20:10]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-03-06 二 20:10]
:END:
*** DONE 基因组整理
CLOSED: [2018-04-07 六 16:52]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-04-07 六 16:52]
:END:
*** DONE NCBI提供的基因组可能同一个基因同时来自正义lian和反义链如果是同一个转录本的话出现两条序列造成RSEM错误
CLOSED: [2018-03-08 四 18:39]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-03-08 四 18:39]
:END:
*** DONE 刘旋给的几个参考基因组整理
CLOSED: [2018-05-02 三 18:36]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-05-02 三 18:36]
:END:
*** DONE 测试邱于涵写的基因组上传接口
CLOSED: [2018-05-07 一 19:24]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-05-07 一 19:24]
:END:
已测试,交给彩萍处理
*** DONE 白菜参考基因组错误查找,修改整理脚本 gtf, fasta去除冗余项
CLOSED: [2018-05-11 五 21:14]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-05-11 五 21:14]
:END:
json 格式检查注意 引号是否齐全
*** DONE 整理冬梅提供的最新基因组和杨帆以前遗留的
CLOSED: [2019-01-26 六 16:04]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-01-26 六 16:04]
:END:
index 错误, 文件目录有时候没有基因组来源目录,需要写一个线下整理的脚本方便以后运行
*** DONE 培训,需要重温之前的TTT培训和 郭权讲的框架的内容
CLOSED: [2019-06-21 Fri 17:25]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-06-21 Fri 17:25]
- State "NEXT" from "DONE" [2019-06-21 Fri 17:25]
- State "DONE" from "PROJECT" [2019-06-21 Fri 17:25]
- State "PROJECT" from "DONE" [2019-06-21 Fri 17:25]
- State "DONE" from "NEXT" [2019-06-21 Fri 17:25]
- State "NEXT" from "DONE" [2019-06-21 Fri 17:25]
- State "DONE" from "PROJECT" [2019-06-21 Fri 17:25]
- State "PROJECT" from "DONE" [2019-06-21 Fri 17:25]
- State "DONE" from "NEXT" [2019-06-21 Fri 17:25]
- State "NEXT" from "DONE" [2019-06-21 Fri 17:24]
- State "DONE" from "NEXT" [2019-06-21 Fri 17:24]
:END:
*** DONE 基因组v2版本处理,后续丘于涵完成后需跟进
CLOSED: [2018-08-02 四 19:35]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-08-02 四 19:35]
:END:
*** DONE 基因组根据GTF过滤biomart 注释,小鼠,人的时候不一致比较多
CLOSED: [2019-01-26 六 16:04]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-01-26 六 16:04]
:END:
*** DONE 基因组部署流程
CLOSED: [2019-06-21 Fri 17:25]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-06-21 Fri 17:25]
:END:
** denovo云平台开发
*** 组装模块
**** DONE TRINITY TOOLS编写
CLOSED: [2017-12-12 Tue 11:26]
:LOGBOOK:
- State "DONE" from "TODO" [2017-12-12 Tue 11:26]
:END:
**** DONE TRINITY 虚拟内存使用研究 /mnt/ilustre/users/sanger-dev/workspace/20171109/Single_de_t3_1/Trinity__3
CLOSED: [2018-01-10 三 22:54]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-10 三 22:54]
:END:
有的命令内存过大每个butterfly 占用8+N g的虚拟内存， 使用parafly容易造成虚拟内存超标把Trinity的butter改成串行
**** DONE Busco TOOLS编写
CLOSED: [2017-12-12 Tue 11:26]
:LOGBOOK:
- State "DONE" from "TODO" [2017-12-12 Tue 11:26]
:END:
**** DONE TRANsrate TOOLS编写
CLOSED: [2017-11-12 Sun 12:44]
:LOGBOOK:
- State "DONE" from "TODO" [2017-11-12 Sun 12:44]
:END:
**** DONE rna fastatat TOOLS编写
CLOSED: [2017-12-12 Tue 11:27]
:LOGBOOK:
- State "DONE" from "TODO" [2017-12-12 Tue 11:27]
:END:
**** DONE 整合组装modules
CLOSED: [2017-12-24 日 20:51]
:LOGBOOK:
- State "DONE" from "NEXT" [2017-12-24 日 20:51]
:END:
**** DONE 组装结果导表
CLOSED: [2017-12-12 Tue 11:27]
:LOGBOOK:
- State "DONE" from "TODO" [2017-12-12 Tue 11:27]
:END:
**** DONE 组装结果导表 数据地址错误、重复到同一个表
CLOSED: [2018-01-02 二 19:11]
:LOGBOOK:
- State "DONE" from "PROJECT" [2018-01-02 二 19:11]
- State "PROJECT" from "DONE" [2018-01-02 二 19:11]
**** DONE 组装结果拆分组装优化一个module，结果评估一个module
CLOSED: [2017-12-24 日 20:52] DEADLINE: <2017-12-13 Wed>
:LOGBOOK:
- State "DONE" from "NEXT" [2017-12-24 日 20:52]
:END:
**** DONE 组装问题如何跳过event
CLOSED: [2017-12-26 二 22:22] SCHEDULED: <2017-12-25 一>
:LOGBOOK:
- State "DONE" from "NEXT" [2017-12-26 二 22:22]
:END:
**** DONE filter unigene on assemble module
SCHEDULED: <2017-12-25 一>
**** DONE 导表函数修改 路径选择添加filter
SCHEDULED: <2017-12-25 一>
**** DONE bug修复cog\kegg\排序，注释表格统计名称排序规范
CLOSED: [2017-12-28 四 22:26]
:LOGBOOK:
- State "DONE" from "NEXT" [2017-12-28 四 22:26]
:END:
**** DONE 修改组装到表函数接受没有优化的结果
CLOSED: [2017-12-28 四 22:27]
:LOGBOOK:
- State "DONE" from "NEXT" [2017-12-28 四 22:27]
:END:
**** DONE 插入基因集删除接口
CLOSED: [2017-12-28 四 22:29]
:LOGBOOK:
- State "DONE" from "NEXT" [2017-12-28 四 22:29]
:END:
**** DONE 插入比对统计表格导表函数
CLOSED: [2017-12-28 四 22:29]
:LOGBOOK:
- State "DONE" from "NEXT" [2017-12-28 四 22:29]
:END:
**** DONE venn图数据没插入因为修改结果名称，导致导表时找不到对应venn文件
CLOSED: [2018-01-10 三 22:57]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-10 三 22:57]
:END:
**** DONE transrate大数据报错研究 snap设置内存相关参数过小具体查看参数snap设置，不写任何参数好像可以
CLOSED: [2018-01-10 三 23:00] SCHEDULED: <2018-01-12 五>
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-10 三 23:00]
- State "NEXT" from "DONE" [2018-01-04 四 22:35]
- State "DONE" from "NEXT" [2018-01-04 四 22:35]
- State "DONE" from "NEXT" [2017-12-29 五 18:42]
:END:
**** DONE transrate大数据报错研究 salmon添加最后一个参数出不了表大量 有一个参数有两个值需要修改ruby脚本 单独运行可以但transrate包装后就不可以了
CLOSED: [2018-01-12 五 19:17]
可能和snap源码有关系
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-12 五 19:17]
- State "NEXT" from "DONE" [2018-01-05 五 19:04]
- State "DONE" from "NEXT" [2017-12-29 五 18:42]
:END:
目前证明是slurm识别虚拟内存并自动控制，可增大内存申请或ssh localhost (需要配置机器)解决
**** DONE Trinity组装分为几个步骤butterfly分机器投递
CLOSED: [2018-01-10 三 22:59]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-10 三 22:59]
:END:
:PROPERTIES:
:ARCHIVE_TIME: 2018-01-24 三 20:26
:ARCHIVE_FILE: ~/work/GTD/todo.org
:ARCHIVE_OLPATH: denovo云平台开发/组装模块
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
***** DONE 分布投递tools
CLOSED: [2018-01-03 三 21:41]
:LOGBOOK:
- State "DONE" from "PROJECT" [2018-01-03 三 21:41]
- State "PROJECT" from "DONE" [2018-01-03 三 21:41]
- State "DONE" from "PROJECT" [2018-01-03 三 21:41]
- State "PROJECT" from "DONE" [2018-01-03 三 21:41]
- State "DONE" from "PROJECT" [2018-01-03 三 21:41]
- State "PROJECT" from "DONE" [2018-01-03 三 21:41]
- State "DONE" from "NEXT" [2018-01-02 二 19:04]
:END:
***** DONE 合并
CLOSED: [2018-01-03 三 21:42]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-03 三 21:42]
:END:
***** DONE module修改
CLOSED: [2018-01-03 三 21:42] SCHEDULED: <2018-01-03 三>
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-03 三 21:42]
:END:
***** DONE 允许出错源目录自动重新运行
***** DONE 测试
CLOSED: [2018-01-20 六 11:48] SCHEDULED: <2018-01-05 五>
:LOGBOOK:
- State "DONE" from "PROJECT" [2018-01-20 六 11:48]
- State "PROJECT" from "DONE" [2018-01-20 六 11:48]
- State "DONE" from "NEXT" [2018-01-20 六 11:48]
:END:
**** DONE Trinity优化随机分布butter命令
CLOSED: [2018-01-18 四 21:38]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-18 四 21:38]
:END:
:PROPERTIES:
:ARCHIVE_TIME: 2018-01-24 三 20:26
:ARCHIVE_FILE: ~/work/GTD/todo.org
:ARCHIVE_OLPATH: denovo云平台开发/组装模块
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
**** DONE 修改云平台denovo导表，测试会重复到两次
CLOSED: [2018-01-26 五 20:41]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-26 五 20:41]
- State "NEXT" from "DONE" [2018-01-26 五 20:41]
- State "DONE" from "PROJECT" [2018-01-26 五 20:41]
- State "PROJECT" from "DONE" [2018-01-26 五 20:41]
:END:
**** DONE 组装结果长度统计表添加表头百分比
CLOSED: [2018-01-18 四 21:39]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-18 四 21:39]
:END:
:PROPERTIES:
:ARCHIVE_TIME: 2018-01-24 三 20:26
:ARCHIVE_FILE: ~/work/GTD/todo.org
:ARCHIVE_OLPATH: denovo云平台开发/组装模块
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
**** DONE 组装sanger trinity修复，不能运行
CLOSED: [2018-01-18 四 21:41]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-18 四 21:41]
:END:
:PROPERTIES:
:ARCHIVE_TIME: 2018-01-24 三 20:26
:ARCHIVE_FILE: ~/work/GTD/todo.org
:ARCHIVE_OLPATH: denovo云平台开发/组装模块
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
perl版本没装threads库，装了后影响注释的COG XML,DBI等pm需要重装
**** DONE 导表函数添加主表main_id
CLOSED: [2018-01-03 三 21:47]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-03 三 21:47]
:END:
:PROPERTIES:
:ARCHIVE_TIME: 2018-01-24 三 20:26
:ARCHIVE_FILE: ~/work/GTD/todo.org
:ARCHIVE_OLPATH: denovo云平台开发/组装模块
:ARCHIVE_CATEGORY: todo
:ARCHIVE_TODO: DONE
:END:
**** DONE 导表函数错误，未做优化时初始化值仍然为优化的结果
CLOSED: [2018-01-26 五 20:28]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-26 五 20:28]
:END:
**** DONE 组装transrate中间重运行会依赖之前的结果，但是结果不完整回报错，表达量计算结果都是NAN
CLOSED: [2018-01-24 三 20:15]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-24 三 20:15]
:END:
**** DONE 组装输入文件不一致 gene2trans文件不对会报Index not found
CLOSED: [2018-01-24 三 20:16]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-01-24 三 20:16]
:END:
**** DONE transrate大数据会占满系统的内存导致卡死，目前修改了使得使用hisat mapping bam替换
CLOSED: [2018-02-02 五 18:31]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-02-02 五 18:31]
:END:
**** DONE 组装支持单向reads组装
CLOSED: [2018-05-02 三 18:46]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-05-02 三 18:46]
:END:
module添加参数\transrate虚拟right.fq因为之前改过接受bam文件会通过, 在gene2trans文件处卡了一会,原因是正常统计和过滤后gene2tran文件不一致忘了之前的设计
**** DONE buscol unigene评估时发现有无优化 结果非常接近
CLOSED: [2018-05-07 一 19:29]
:LOGBOOK:
- State "DONE" from "NEXT" [2018-05-07 一 19:29]
:END:
**** DONE 组装线上线下比较结果
CLOSED: [2021-12-24 五 08:38] SCHEDULED: <2018-01-29 一>
- State "NEXT" from "TODO" [2021-12-24 五 08:38]
- State "TODO" from "TODO" [2021-12-22 三 08:19]
- State "TODO" from "DONE" [2021-12-22 三 08:19]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-01-26 六 16:08]
:END:
有的结果非常碎，暂时无法解决
**** DONE 比对率统计的reads数量少一半
CLOSED: [2019-01-26 六 16:07]
:LOGBOOK:
- State "DONE" from "NEXT" [2019-01-26 六 16:07]
:END:
**** DONE denovo组装时如果重新跑distribue的步骤complete的也会作为一个tools跑
CLOSED: [2019-01-26 六 16:08]