Question: MToolBox.sh: line 173: check_files.py: command not found
0
gravatar for Cindy
11 months ago by
Cindy10
Cindy10 wrote:

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

sequencing • 316 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by Cindy10
1

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

ADD REPLYlink modified 11 months ago • written 11 months ago by genomax46k
1
gravatar for Cindy
11 months ago by
Cindy10
Cindy10 wrote:

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!

ADD COMMENTlink written 11 months ago by Cindy10

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.

ADD REPLYlink modified 11 months ago • written 11 months ago by jrj.healey3.8k

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

ADD REPLYlink written 11 months ago by Cindy10

Is that the exact (and only) error?

ADD REPLYlink written 11 months ago by genomax46k

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.

ADD REPLYlink written 11 months ago by Cindy10
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