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MGI-tech-bioinformatics / DNBelab_C_Series_HT_scRNA-analysis-software

An open source and flexible pipeline to analysis high-throughput DNBelab C Series single-cell RNA datasets
MIT License
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DNBCtools主程序（count）报错 #24

Closed yuanmaomao2023 closed 5 months ago

yuanmaomao2023 commented 1 year ago

您好，我在使用DNBCtools进行主程序运行时，中生成filter_matrix过程中出现报错，报错内容如下： 2023-07-30 12:06:05,074 - count - INFO - Promgram start... 2023-07-30 12:06:05,074 - count - INFO - /../bin/python /../DNBC4tools/lib/python3.8/site-packages/DNBC4tools/rna/cellMerge.py --indir /../02.count --name xxx Traceback (most recent call last): File "/../python3.8/site-packages/pandas/core/indexes/base.py", line 3652, in get_loc return self._engine.get_loc(casted_key) File "pandas/_libs/index.pyx", line 147, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 176, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 7080, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 7088, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'index'

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/../DNBC4tools/lib/python3.8/site-packages/DNBC4tools/rna/cellMerge.py", line 95, in figtable['index'] = figtable['index'].astype(int) File "/../python3.8/site-packages/pandas/core/frame.py", line 3761, in getitem indexer = self.columns.get_loc(key) File "/../python3.8/site-packages/pandas/core/indexes/base.py", line 3654, in get_loc raise KeyError(key) from err KeyError: 'index' Traceback (most recent call last): File "/../DNBC4tools/bin/DNBC4tools", line 8, in sys.exit(main()) File "/../DNBC4tools/lib/python3.8/site-packages/DNBC4tools/DNBC4tools.py", line 43, in main args.func(args) File "/../DNBC4tools/lib/python3.8/site-packages/DNBC4tools/tools/count.py", line 71, in count Count(args).run() File "/../DNBC4tools/lib/python3.8/site-packages/DNBC4tools/tools/count.py", line 59, in run logging_call(CellMerge_cmd,'count',self.outdir) File "/../DNBC4tools/lib/python3.8/site-packages/DNBC4tools/tools/utils.py", line 50, in logging_call check_call(popenargs,shell=True) File "/../DNBC4tools/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/../DNBC4tools/bin/python /../DNBC4tools/lib/python3.8/site-packages/DNBC4tools/rna/cellMerge.py --indir /../02.count --name xx returned non-zero exit status 1.

麻烦您可以帮我看一下吗？尝试过pandas升级，但是还是出现同样的报错，冒昧打扰，非常感谢！

lishuangshuang0616 commented 1 year ago

能截图一下你的02.count生成的目录内的文件吗？特别是combined_list.txt这个文件能否看下内容。

yuanmaomao2023 commented 1 year ago

非常感谢能得到您的回复， 以下是我的02.count文件内容和combined.list文件具体内容

再次感谢您的回复，也很抱歉周末时间贸然打扰您，祝您生活愉快，一切顺利。 袁梦丽

@. | ---- 回复的原邮件 ---- | 发件人 | @.> | | 发送日期 | 2023年7月30日 22:07 | | 收件人 | @.> | | 抄送人 | @.> , @.***> | | 主题 | Re: [MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software] DNBCtools主程序（count）报错 (Issue #24) |

能截图一下你的02.count生成的目录内的文件吗？特别是combined_list.txt这个文件能否看下内容。

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.

lishuangshuang0616 commented 1 year ago

我这边看不到你发的图片 你看看是不是没传过来 image

yuanmaomao2023 commented 1 year ago

老师您好， 我把图片放在附件里，麻烦您再帮我看一下吧。

袁梦丽

@. | ---- 回复的原邮件 ---- | 发件人 | @.> | | 发送日期 | 2023年7月31日 11:32 | | 收件人 | @.> | | 抄送人 | @.> , @.***> | | 主题 | Re: [MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software] DNBCtools主程序（count）报错 (Issue #24) |

我这边看不到你发的图片 你看看是不是没传过来

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

lishuangshuang0616 commented 1 year ago

抱歉我还是没看到，你邮件和我沟通吧 lishuangshuang3@mgi-tech.com