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gavinha avatar gavinha commented on August 20, 2024

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?

counts <- loadReadCountsFromWig(tumour_reads, chrs = chrs, gc = gc, map = map,

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.

counts <- correctReadCounts(counts, chrNormalize = chrNormalize)

Let me know what you find.

Best,
Gavin

from ichorcna.

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