Comments (1)
Hi @smangul1
This error usually occurs when there there are either (1) too few bins remaining after filtering or (2) the coverage is too low for the loess curve fitting. Do you know the sequencing coverage of your sample?
Have you had any other samples run to completion and that this is just an exception?
If it is because of bins being filtered out, can you try to debug the the R script right before this line and check that tumour_reads
contains all the chromosomes and number of rows matching what you expect?
ichorCNA/scripts/runIchorCNA.R
Line 172 in f2dc657
If that doesn't reveal anything, can you debug into the function, right before this line and see if counts
is not empty or lacking rows.
Line 102 in f2dc657
Let me know what you find.
Best,
Gavin
from ichorcna.
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