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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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DNBC4tools 主程序运行时报错 #15

Closed luyz1998 closed 1 year ago

luyz1998 commented 1 year ago

作者您好!我在使用DNBC4tools （2.0.7）主程序run时，运行到生成raw_matrix目录时产生报错： Traceback (most recent call last): File "/gpfs/home/luyz/biosoft/miniconda3/envs/DNBC4tools/bin/DNBC4tools", line 8, in sys.exit(main()) File "/gpfs/home/luyz/biosoft/miniconda3/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/DNBC4tools.py", line 43, in mainargs.func(args) File "/gpfs/home/luyz/biosoft/miniconda3/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/tools/data.py", line 47, in data Data(args).run() File "/gpfs/home/luyz/biosoft/miniconda3/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/tools/data.py", line 42, in run logging_call(raw_matrix_cmd,'data',self.outdir) File "/gpfs/home/luyz/biosoft/miniconda3/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/tools/utils.py", line 50, in logging_call check_call(popenargs,shell=True) File "/gpfs/home/luyz/biosoft/miniconda3/envs/DNBC4tools/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '/gpfs/home/luyz/biosoft/miniconda3/envs/DNBC4tools/lib/python3.8/site-packages/DNBC4tools/soft/PISA count -@ 32 -cb CB -anno-tag GN -umi UB -outdir /gpfs/home/luyz/work/singlecell/midaiwu/dnbflow/STM/stomach/01.data/raw_matrix /gpfs/home/luyz/work/singlecell/midaiwu/dnbflow/STM/stomach/01.data/final_sorted.bam' returned non-zero exit status 1. 多个样本运行都出现了这个报错，请问是什么原因呢？

lishuangshuang0616 commented 1 year ago

Can you take a screenshot of the 01.data directory, I need to confirm that there is no problem with the steps before the PISA count @luyz1998

luyz1998 commented 1 year ago

image

lishuangshuang0616 commented 1 year ago

From the screenshots, it seems that there is no problem with the previous analysis, but why the time for mapping and annotation is not long, but the time for the samtools sort to generate final_sorted.bam is indeed very long, which is quite strange. You can use samtools quickcheck to check the integrity of final_sorted.bam. Is there any other errors before the error message? @luyz1998

luyz1998 commented 1 year ago

samtools quickcheck的结果没问题，不知道是不是我们服务器的一些故障导致的个人账号下一些软件的损坏（有其他软件因损坏不能正常运行），我正在尝试重装软件之后再运行任务，如果还是同样报错再与您联系！非常感谢！

lishuangshuang0616 commented 1 year ago

好的，也可以单独跑下PISA count那个步骤来看下是否还会报错。 @luyz1998

luyz1998 commented 1 year ago

image 重装软件后单独运行PISA count产生了不同的报错，显示如上。

lishuangshuang0616 commented 1 year ago

看下anno_report.csv

luyz1998 commented 1 year ago

image

lishuangshuang0616 commented 1 year ago

看来你的gtf文件有点问题 @luyz1998

luyz1998 commented 1 year ago

非常感谢回答！已找到问题所在！