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sagarutturkar / CNVkit_pipeline

Pipeline for CNVkit
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Error in step 1 #1

Open vaishmanobala opened 2 years ago

vaishmanobala commented 2 years ago

Hi,

I tried running as per the instruction. all i get is this error Use of uninitialized value $tumor in concatenation (.) or string at /root/CNVkit_pipeline/lib/Module/CNVkit.pm line 61.

Would also like to have a little clarification for Tumor Only samples.

Could you please help me with the pipeline with TO samples.

sagarutturkar commented 2 years ago
  1. Did you run: dos2unix prepare_CNVkit.sh.txt?
  2. Do you see directories with exact names - input, output and submission_files?
  3. The samples should have strict naming as *_tumor.bam and should be placed inside the input directory.
  4. The submission files follow the HPC #PBS code and designed to run at Purdue University. You can copy the individual commands and those should work on your system. This is designed to run with WGS data, check if all parameters are as expected for you data-type.
vaishmanobala commented 2 years ago

Hi,

All the points are noted and followed, except for the 4th one.

The data here I'm trying to is WES.

The discrepancy must be because of that.

It would be great if you can also include option for WES datasets.

Thanks & regards!

sagarutturkar commented 2 years ago

It works fine at my end with above steps. Please re-check at your end, may be something wrong with your directory structure. You can run ls -R and share the output. Also, send the CNVkit.sh file under submission_files directory.

You have to check on CNVkit website how to run it for WES data. It should only be changing couple of options. You can modify the CNVkit.sub file with relevant options.