dnbc4tools run 报错

[owo12138]

你好，我在运行run步骤遇到了以下问题 这是我的运行代码 ~/miniconda3/envs/dnbc4tools/bin/dnbc4tools rna run --cDNAfastq1 /date/xiezhixing/cDNA/AS001_S1_L001_1.fq.gz --cDNAfastq2 /date/xiezhixing/cDNA/AS001_S1_L001_2.fq.gz --oligofastq1 /date/xiezhixing/oligo/AS001_S1_L001_1.fq.gz --oligofastq2 /date/xiezhixing/oligo/AS001_S1_L001_2.fq.gz --genomeDir /date/xiezhixing --name as --threads 10 以下是报错 `The chemistry(darkreaction) automatically determined in cDNA : darkreaction The chemistry(darkreaction) automatically determined in oligoR1 : darkreaction The chemistry(darkreaction) automatically determined in oligoR2 : darkreaction

2024-01-20 23:45:13 Processing cDNA library barcodes and aligning.

2024-01-20 23:45:13 Processing oligo library barcodes. 2024-01-20 23:45:48,781 - data - ERROR Command failed with exit code 1 2024-01-20 23:45:48,782 - data - ERROR 2024-1-20 23:45:13 ..... started STAR run Jan 20 23:45:13 ..... loading genome Error code: SAW-A10151

2024-01-20 23:50:56 Annotating BAM files. 2024-01-20 23:50:56,850 - data - ERROR Command failed with exit code -11 2024-01-20 23:50:56,851 - data - ERROR [W::hts_set_opt] Cannot change block size for this format

2024-01-20 23:50:56,860 - data - ERROR Command failed with exit code 1 2024-01-20 23:50:56,860 - data - ERROR [E::hts_open_format] Failed to open file "/date/xiezhixing/as/01.data/final.bam" : No such file or directory samtools sort: can't open "/date/xiezhixing/as/01.data/final.bam": No such file or directory

2024-01-20 23:50:56 Calculating bead similarity and merging beads. Traceback (most recent call last): File "/share/home/xiezhixing/miniconda3/envs/dnbc4tools/bin/dnbc4rna", line 8, in sys.exit(main()) File "/share/home/xiezhixing/miniconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/rna/dnbc4rna.py", line 38, in main args.func(args) File "/share/home/xiezhixing/miniconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/rna/count.py", line 220, in count Count(args).run() File "/share/home/xiezhixing/miniconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/rna/count.py", line 58, in run from dnbc4tools.rna.src.oligo_filter import oligo_combine,cut_umi File "/share/home/xiezhixing/miniconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/rna/src/oligo_filter.py", line 13, in import polars as pl ModuleNotFoundError: No module named 'polars' Traceback (most recent call last): File "/share/home/xiezhixing/miniconda3/envs/dnbc4tools/bin/dnbc4tools", line 8, in sys.exit(main()) File "/share/home/xiezhixing/miniconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/dnbc4tools.py", line 58, in main args.func(args) File "/share/home/xiezhixing/miniconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/rna/run.py", line 105, in run Runpipe(args).runpipe() File "/share/home/xiezhixing/miniconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/rna/run.py", line 92, in runpipe start_print_cmd(pipecmd,os.path.join(self.outdir,self.name)) File "/share/home/xiezhixing/miniconda3/envs/dnbc4tools/lib/python3.8/site-packages/dnbc4tools/tools/utils.py", line 38, in start_print_cmd subprocess.check_call(arg, shell=True) File "/share/home/xiezhixing/miniconda3/envs/dnbc4tools/lib/python3.8/subprocess.py", line 364, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command 'dnbc4rna count --name as --calling_method emptydrops --expectcells 3000 --forcecells 0 --minumi 1000 --threads 10 --outdir /date/xiezhixing' returned non-zero exit status 1. ` 这是我的存储文件对应的目录 以上代码及文件是存储在服务器中调用并运行的 请问要如何解决呢

[owo12138]

是不是因为内存不够呢，我分配了300g内存。文件cDNA总共有80g大小

[lishuangshuang0616]

After looking at your directory, it seems that there is a problem with your mkref database. You can check whether there is an error when building the database.

[owo12138]

这是我利用quick start里面的人源基因组数据生成的ref.json 请问如何检查呢？

[lishuangshuang0616]

检查一下这些文件都有吗，红框框出来的

[owo12138]

都有的

[owo12138]

另外就是我考虑是dnbc4tools没安装完全的原因，我重新安装了，但是在安装过程一直报错

[owo12138]

安装完环境可以激活dnbc4tools环境， 但是无法调用dnbc4tools 显示no command

[owo12138]

报错如下

[lishuangshuang0616]

你这个是因为这个包无法安装，尝试在dnbc4tools.yaml开头几行修改下，给镜像试试

name: dnbc4tools
channels:
  - http://mirrors.bfsu.edu.cn/anaconda/pkgs/r/
  - http://mirrors.bfsu.edu.cn/anaconda/pkgs/main/
  - http://mirrors.bfsu.edu.cn/anaconda/pkgs/free/
  - http://mirrors.bfsu.edu.cn/anaconda/cloud/conda-forge/
  - http://mirrors.bfsu.edu.cn/anaconda/cloud/bioconda/
  - bioconda
  - conda-forge
  - http://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/msys2/
dependencies:

[lishuangshuang0616]

顺便截图下01.data内的cDNA_para、cDNAin1和cDNAin2的内容

[owo12138]

[owo12138]

现在用channel重新下载，仍然出现报错

[owo12138]

我试图更新这个yaml，但是又遇到以下报错

[lishuangshuang0616]

把01.data内的cDNA_para、cDNAin1和cDNAin2文件发我吧 如果之前环境dnbc4tools 的command能使用，先不忙着安装了，这个包目前安装的镜像有点问题。

[owo12138]

重新安装一遍后的command也不能用了

[lishuangshuang0616]

原本的还在不

[owo12138]

comman和环境不在了，不过生成的数据还在

[lishuangshuang0616]

如果实在装不上，看下能否使用docker或者singularity试试

[owo12138]

cDNAin1.zip

[owo12138]

docker因为服务器无sudo权限，我试试singularity 请问singularity中的database 和data文件夹里面需要有什么呢

[lishuangshuang0616]

export只需要把你所有需要在容器中映射的目录放进去进行了，比如你的database的目录，你的文件目录，你的结果目录等等，只要需要挂载映射的都放上去进行

[owo12138]

但是似乎还是因为源的原因，这个singularity也下载不了

[owo12138]

于是我在自己windox电脑上加载wsl 运行docker sh如上

报错如上

对应工作目录及对应文件如上

[lishuangshuang0616]

但是似乎还是因为源的原因，这个singularity也下载不了

多试几次呢？

[lishuangshuang0616]

docker的话你输入命令行呢，不用bash文件。

$Database_LOCAL:/database，直接替换$Database_LOCAL试试

[owo12138]

singularity我在两个服务器上运行了都是不行

[owo12138]

docker的话你输入命令行呢，不用bash文件。

$Database_LOCAL:/database，直接替换$Database_LOCAL试试

那么我的路径应该如何输入呢？，这里我的路径应该替换在哪里呢？

[lishuangshuang0616]

docker run -P -v /mnt/d/scrna/dnbc4/Database:/database -v 这样

[owo12138]

我进行替换后仍然出现报错

[lishuangshuang0616]

没有问题，直接在rna后面加命令就行，如果不加命令就加--help

[owo12138]

似乎还是不行？

[lishuangshuang0616]

你的文件需要路径，你挂在后的路径比如/database/genes.filter.gtf

[owo12138]

似乎仍然不可以

[lishuangshuang0616]

/database

[owo12138]

我两种都试过了之前

[lishuangshuang0616]

你需要确定/mnt/d/scrna/dnbc4/Database目录内存在gtf文件且不是链接文件

[ultraypy]