MToolBox.sh: line 173: check_files.py: command not found

Question

[Cindy]

Anyone use MToolBox to analysis mtDNA sequencing data? When I run MToolBox, it always shows this error. "bash MToolBox.sh -i config.sh

setup.sh file not found. Setting MToolBox environment sourcing conf.sh file setting up MToolBox variables in config file ... ...done Check python version... (2.7 required) OK. Checking files to be used in MToolBox execution... MToolBox.sh: line 173: check_files.py: command not found"

But setup.sh is in the same folder. How can I fix this issue? Thanks

[GenoMax]

Can you add at that folder to $PATH (export PATH=$PATH:/path_to/MToolBox_folder (replace with a real path)?

Answer 1

[Cindy]

Yes. It works now. I am so stupid, I did't know the PATH is the issue since I cd to the MToolBox folder. Thanks!

[Joe]

Even if you are in the folder where the file exists, if the folder isn't in the PATH, you would have to call the script/program with a filepath, e.g. $ ./setup.sh or it's full path, $ setup.sh wouldn't be sufficient.

[Cindy]

After a couple of hours running, it showed another error: IndelRealigner command not found. I have already cp theGenomeAnalysisTK.jar to MToolBox/ext_tools. Any idea? Thanks

[GenoMax]

Is that the exact (and only) error?

[Cindy]

Yes. It is. GATK and SamToFastq.jar are in the same folder (ext_tools). fastq files have been successfully generated. But IndelRealigner command not found.