====售后技术magic报错排查====


1. 账号密码

主机：172.17.244.172

账号：weile

密码：novo2017

2. 云工具路径

/data3/ngs/tools/{邮箱}/{任务名称}_script

3. 云分析路径

/data3/ngs/{magic编号}/{任务名称}_script

4. 脚本名称

sh的脚本命名：任务名+.sh

5. 报错类型

（1） magic平台没有刷出来脚本

特征：只有main.log没有生成sh文件。

报错原因：由于参数不对，导致流程没有刷出来的脚本。

解决方案：查阅配置文件project.ini和project.json是否正确。

报错检查：
<code>
/data3/ngs/X101SC21122050-Z01-J001/plt300genes_script/main.log

[out]

[error]
Traceback (most recent call last):
  File "/NGS/ngs/pipline_v1//med_ref/buildConfig_med.py", line 38, in <module>
    genome_version = cf.get('basic','genome_version')
  File "/data/NGS_RNA/software/miniconda3/envs/python_2.7/lib/python2.7/ConfigParser.py", line 618, in get
    raise NoOptionError(option, section)
ConfigParser.NoOptionError: No option 'genome_version' in section: 'basic'
sh: /data3/ngs/X101SC21122050-Z01-J001/plt300genes_script/plt300genes.sh: No such file or directory

</code>
<code>
X101SC23020724-Z01-J001/AAAA_script/main.log
[out]

[error]
Traceback (most recent call last):
  File "/NGS/ngs/pipline_v1//no_ref/buildConfig_noref.py", line 37, in <module>
    specie = kaas_dic[specie]
KeyError: 'all'
sh: /data3/ngs/X101SC23020724-Z01-J001/AAAA_script/AAAA.sh: No such file or directory
</code>
（2）magic分析过程中报错

特征：如果有main.log，也有sh文件。

报错原因：流程刷出来脚本，但是分析过程中报错，常见原因有输入文件不正确。

解决方案：根据magic任务提交页面确定输入文件的形式，再查阅老师提供文件，确实哪里出了问题。

报错检查：从上查阅main.log是否有Error/Execution halted/IOError字眼。如果有以上字眼可以查阅后面的报错信息。

例子1：
<code>
Error in hclust(d, method = method) : must have n >= 2 objects to cluster
/data3/ngs/X101SC20070730-Z01-J001-B1/pca_1_script/main.log
Traceback (most recent call last):
  File "/data/NGS/ngs/ref_v2/prepare_pca.py", line 9, in <module>
    data = df[sample_list].query(con1)
  File "/data/RNA/software/python-2.7.10/lib/python2.7/site-packages/pandas/core/frame.py", line 2056, in __getitem__
    return self._getitem_array(key)
  File "/data/RNA/software/python-2.7.10/lib/python2.7/site-packages/pandas/core/frame.py", line 2100, in _getitem_array
    indexer = self.loc._convert_to_indexer(key, axis=1)
  File "/data/RNA/software/python-2.7.10/lib/python2.7/site-packages/pandas/core/indexing.py", line 1231, in _convert_to_indexer
    raise KeyError('%s not in index' % objarr[mask])
KeyError: "['2642088.0' '2642084.0' '379431.0' ..., '108696085.0' '108708407.0'\n '108718027.0'] not in index"
Error in file(file, "rt") : cannot open the connection
Calls: read.delim -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/data3/ngs/X101SC20070730-Z01-J001-B1/pca_1_script//pca_fpkm.xls': No such file or directory
Execution halted
Loading required package: methods
Error in file(file, "rt") : cannot open the connection
Calls: read.delim -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/data3/ngs/X101SC20070730-Z01-J001-B1/pca_1_script//pca_fpkm.xls': No such file or directory
Execution halted

</code>
报错原因输入文件不对：

例子2：
<code>
/data3/ngs/X101SC22125287-Z01-J003_sRNA/adwees_script/main.log
[out]
adwees
id type: smallRNA ID
1
2
  adding: adwees_result/ (stored 0%)
  adding: adwees_result/GO/ (stored 0%)
success

[error]
dos2unix: converting file /data3/ngs/X101SC22125287-Z01-J003_sRNA/adwees_script//turn_inputFile.txt to Unix format ...
Error in ids$gene_id : $ operator is invalid for atomic vectors
Calls: [ -> [.data.frame -> which -> %in%
Execution halted
Error in file(file, "rt") : cannot open the connection
</code>
报错原因输入文件的表头不对。

tips：但是下面的报错不会影响任务正确行：

<code>
[error]
dos2unix: converting file turn_rbms.xlsx to Unix format ...

cp: cannot stat ‘/NGS/ngs/pipline_v1/new_ref/readme/cluster_readme.txt’: No such file or directory
rm: cannot remove ‘/data3/ngs/X101SC22080067-Z01-J003/new/RBMS//RBMS_result/../RBMS_script’: No such file or directory
rm: cannot remove ‘/NGS/ngs/pipline_v1/VennDiagram2022*’: No such file or directory
rm: cannot remove ‘/NGS/ngs/pipline_v1/Rplots.pdf’: No such file or directory
</code>

还有就是警告信息，这种也不会引起任务中断：
<code>
Warning message:
In min(na.omit(unlist(as.list(union)))) :
  no non-missing arguments to min; returning Inf
/data3/ngs/X101SC22080067-Z01-J003/RBMS_script/main.log
</code>

如果解决不了，需要派单，派单时必要内容如下：

|平台类型|账号|任务名|报错描述|
|云工具|邮箱|tack_name|示例：任务运行结束后Magic交互页面不能实现对通路的筛选做图。截图见附件。|
|云分析|magic编号|tack_name|同上|