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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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custom genome and sex chromosome error #669

Open acontrerasg opened 2 years ago

acontrerasg commented 2 years ago

Hello, I am running this pipeline with the batch command and a custom genome that lacks sex chromosomes. The batch command lacks the option '-x' to specify to skip the X chromosome search. After a run , which appears to have produced a satisfactory output, in the log file there is this statement produced by the ./cnvlib/cnary.py script:

No X found in sample; is the input truncated?

My question is, can I ignore this error and go ahead with the results, which look normal. Or shall I ran all steps manually to ensure no funny calls have been made?

Thank you!

cnvkit version is 0.9.9

tetedange13 commented 2 years ago

Hi @acontrerasg ,

Not an author of CNVkit, but have you run batch with its --diagram option? => If yes, could you please confirm that this No X found message is gone when you run batch without --diagram

Digging into cnvlib/batch.py code, it looks like this error is raised by cnarr.shift_xx() method (which is called trying to plot ideogram mostly) => To sum up it should be fine to ignore this error (even I could not be 100% assertive about that)

Hope this helped. Have a nice day. Felix.

acontrerasg commented 2 years ago

Hello Felix,

yes I am running without that option , also without --scatter option.
I also think is safe to ignore, mostly because it will try to balance out CNV in that particular chromosome but shouldn't affect the others. No?

Thanks for your help!