Hello. Thank you for providing the analysis procedures and detailed documentation. I am studying the analysis process of seq-scope data and trying to analyze the demo data using the instructions in your documentation, but I encountered an error during the dry-run. I followed the code installation instructions on your website. Here is the runing code and error message.
# paths
smk_dir=/home/huanmu/software/NovaScope
job_dir=/public/huanmu/Spatial/seq-scope/novascope/demo_data/B08Ctest
snakemake -s $smk_dir/NovaScope.smk --rerun-incomplete -d $job_dir --dry-run -p
KeyError in file /home/huanmu/software/NovaScope/NovaScope.smk, line 195:
'sge_format'
File "/home/huanmu/software/NovaScope/NovaScope.smk", line 195, in <module>
File "/home/huanmu/software/NovaScope/scripts/pipe_condout_novascope.py", line 276, in outfnlist_by_seg
File "/home/huanmu/miniconda3/envs/snakemake-env/lib/python3.9/site-packages/pandas/core/frame.py", line 4102, in __getitem__
File "/home/huanmu/miniconda3/envs/snakemake-env/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3812, in get_loc
The config_job.yaml is located in the B08Ctest directory, and its content is modified based on the testrun file. I believe that my absolute path is correct. The config_env.yaml is similar, only annotated envmodules ,and its content is as follows.
## Path to the dependent software tools
## Please replace /path/to the actual path to the binary of the software tools
tools:
spatula: "/home/huanmu/software/spatula/"
samtools: "/home/huanmu/miniconda3/envs/snakemake-env/bin/samtools"
star: "/home/huanmu/miniconda3/envs/snakemake-env/bin/STAR"
# tools-specific configuration:
# If your system supports module loading, you may specify the module names for the required software tools.
#envmodules:
# python: "python/3.9.12"
# gcc: "gcc/10.3.0"
# gdal: "gdal/3.5.1"
# imagemagick: "imagemagick/7.1.0-25.lua"
## Path to the reference genomes
## For each species, you need to provide the path to the STAR index
ref:
align:
mouse: "/home/huanmu/genomics/CellRanger/refdata-gex-GRCm39-2024-A/star_2_7_11b"
human: "/home/huanmu/genomics/CellRanger/refdata-gex-GRCh38-2024-A/star_2_7_11b"
## you may add other reference data here
## Path to the python virtual environment
pyenv: "/home/huanmu/pyvenvs/novascope_venv/"
What could be the possible cause of this error? Is it something that I overlooked? Or is it because I installed the dependency tools using the conda environment? If you can provide assistance, I would greatly appreciate it.
Hello. Thank you for providing the analysis procedures and detailed documentation. I am studying the analysis process of seq-scope data and trying to analyze the demo data using the instructions in your documentation, but I encountered an error during the dry-run. I followed the code installation instructions on your website. Here is the runing code and error message.
The
config_job.yamlis located in the B08Ctest directory, and its content is modified based on the testrun file. I believe that my absolute path is correct. Theconfig_env.yamlis similar, only annotatedenvmodules,and its content is as follows.What could be the possible cause of this error? Is it something that I overlooked? Or is it because I installed the dependency tools using the conda environment? If you can provide assistance, I would greatly appreciate it.