ValueError: Reference is missing 1 bins found in xx.sort_dedup

[asmlgkj]

Thanks a lor for this powerful tool for cnv when run tumor only mode, it shows this.

but rerun, it disappears, is there any reason

[tetedange13]

Hi @asmlgkj,

Not an author of CNVkit but looking into the code, this specific error is raised during fix step here: https://github.com/etal/cnvkit/blob/36ce0dabf1772fd439f60a0410bc66be953a513c/cnvlib/fix.py#L142-L146

=> Comment at L142 says "check for sign that wrong reference was used" => So that is probably what happened: you gave CNVkit a wrong reference and gave the proper one when you re-run (so error disapppered) => "wrong" here meaning a "reference.cnn" file with a region/bin not matching your target or antitarget ".cnn" files

But without further details on exact CNVkit command-lines you ran, it will be hard to help you more...

Hope this helps. Felix.

[asmlgkj]

thanks a lot, after re-run the command, it succeed. I do not know why, is there any possible reason

[asmlgkj]

@tetedange13 Thanks a lot, I do not change any file (add in or delete or reviese file)