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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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Error in loadNamespace(x) : there is no package called ‘argparse’ #40

Closed uddamvathanak closed 2 months ago

uddamvathanak commented 7 months ago

2023-11-23 02:38:44 Generating the raw expression matrix. 2023-11-23 02:47:09,736 - count - ERROR Command failed with exit code 1 2023-11-23 02:47:09,737 - count - ERROR Error in loadNamespace(x) : there is no package called ‘argparse’ Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart Execution halted

2023-11-23 02:47:09 Generating the filtered expression matrix. 2023-11-23 02:47:09,762 - count - ERROR Command failed with exit code 1 2023-11-23 02:47:09,762 - count - ERROR [error] [func: dict_read, line: 212] /disco_500t/rom/Colab/K0_control_processed/02.count/beads_barcodes.txt : No such file or directory.

lishuangshuang0616 commented 7 months ago

The error message suggests that the R package argparse is not installed. To resolve this, you can run the following commands in the dnbc4tools environment:

conda activate dnbc4tools
conda install r-argparse

To re-run the dnbc4tools rna run, you only need to reanalyze the broken part, u can add the parameters --process count,analysis,report.

uddamvathanak commented 7 months ago

Thank you so much. So the reason I'm having this issue is that the installation process is not suitable for Miniforge installation and so I need to reinstall everything from scratch and debug by the error message. If possible please have the miniforge version of Conda. I'm from SIgN and need to run the pipeline for processing the data.

lishuangshuang0616 commented 7 months ago

Thank you for reminding me about the Miniforge installation requirements. I will consider it.