Error running the pipeline expected str, bytes or os.PathLike object, not NoneType

[nishah-27]

I am new to STpipeline, and I am trying to run the mentioned command

st_pipeline_run.py --expName test --ref-map path_to_reference --log-file log_file.txt --output-folder path_to_reference --ref-annotation Homo_sapiens.GRCh38.110.gtf path_to_SRRid/SRRid.fastq path_to_SRRid/SRRid_2.fastq

This is the error that I faced - Error running the pipeline expected str, bytes or os.PathLike object, not NoneType - st_pipeline_run.py path_to_SRRid/SRRid_1.fastq path_to_SRRid/ /SRRid_2.fastq --expName test

I am encountering the same error with only fastq files and exp name. Any help regarding this would be highly appreciated. Thank you.

[jfnavarro]

Hello! I suggest that you use the more up-to-date repository https://github.com/jfnavarro/st_pipeline

The arguments must be before the input files always. Also, make sure that path_to_SRRid/SRRid.fastq path_to_SRRid/SRRid_2.fastq are correct paths that are reachable from where you invoke the pipeline. It's generally safer to use absolute paths.

[nishah-27]

Hello, 1.8.1 is our version of the st_pipeline. st_pipeline_run.py --version st_pipeline_run.py 1.8.1

The path that we used, was rechecked and it was confirmed that it was an absolute path.