RUN error: count - ERROR Command failed with exit code 134

[zengh58]

Hi, I encountered some errors when running the code below:

dnbc4tools rna run   --cDNAfastq1 cDNAlib-A3_raw_1.fq.gz   --cDNAfastq2 cDNAlib-A3_raw_2.fq.gz   --oligofastq1 oligolib-A3_raw_1.fq.gz   --oligofastq2 oligolib-A3_raw_2.fq.gz   --genomeDir ref   --name A3 --threads 50

The error is depicted in the picture:

I noticed a similar issue reported by others. However, based on the solution provided, my "CB_UB_count.txt" file is not empty. Thus, I'm unsure about the exact problem or what steps to take next. Could you offer any guidance? Thank you!

[lishuangshuang0616]

Screenshot 01.data

[zengh58]

[lishuangshuang0616]

ls -lh，look at the storage space of the file and the contents of the _alignmentreport.csv and _annoreport.csv files.

[zengh58]

01.data:

alignment_report.csv：

anno_report.csv：

[lishuangshuang0616]

There is something wrong with your gtf file。

[zengh58]

Thank you for your solution! I have two GTF files; this time, I used the first one. I thought it meets the conditions mentioned above. However, if the first one is not okay, is the other one correct? Thank you!

The first one:

The other one:

[zengh58]

Oh, I must mention that, initially, I ran the code from your tutorial: dnbc4tools tools mkgtf --ingtf ref.gtf --output genes.filter.gtf --type gene_type However, the output file genes.filter.gtf is empty, and subsequent code failed. Consequently, I skipped that step and used the original GTF as the input for the "dnbc4tools rna run". I'm uncertain if this has any impact.

[lishuangshuang0616]

The filtering step is optional. The other one is OK

[zengh58]

Thank you for your help! I'll give it a try.

[zengh58]

Excuse me, I used the other GTF file, but I encountered another error...

[lishuangshuang0616]

Your environment is not installed properly. You can test whether the R library (DropletUtils) is installed successfully. If the installation is not successful, reinstall dnbc4tools. If there is no problem with the installation, it may be that the .Rprofile file exists in the home directory or the R-related path exists in ~/.bashrc, causing the location of the identified package to be specified. if reinstall, you can modify the mirror in yaml to ensure that the installation does not go wrong.

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:

Since you have completed the analysis of 01.data, add --process count, analysis, report when re-analyzing to skip the completed steps.

[zengh58]

Thank you! I've resolved the issue. When I tried to load DropletUtils, it prompted me about the missing S4Arrays package. After installing it, everything worked smoothly, and the code is now running fine.