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Runtime error at the Usage steps: "ValueError: View table is out of the bounds of chromosomes in cooler." #5

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hisakatha opened this issue Sep 16, 2022 · 1 comment

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@hisakatha
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Hello.
I followed the Usage section in the README.
Specifically, I cloned this repository and rewrote the following four lines in config/config.yml to point at my local hg38 files.

path_genome_folder: /Users/ilya/Projects/quaich/resources/genome/
path_genome_fasta: /Users/ilya/Projects/quaich/resources/genome/hg38/hg38.fa
chromsizes: /Users/ilya/Projects/quaich/resources/genome/hg38/hg38_chromsizes.txt
view: /Users/ilya/Projects/quaich/resources/test_view.txt

Then, I proceeded to Step 4.
Dry-run snakemake --use-conda --configfile config/config.yml -n has been done successfully.
However, snakemake --use-conda --configfile config/config.yml --cores 10 raises the following error from cooltools/lib/checks.py:
ValueError: View table is out of the bounds of chromosomes in cooler.

The version of cooltools after the Usage Step 3 is 0.5.1.

I would appreciate if I could resolve this error.
Do I have to change more lines in the config files?

@yardimcilab
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I also had this problem. For context, my mcools are generated via hic2mcool from .hic files. hic2mcool has problems converting the latest .hic file format version to .mcool. The bug I know about is that chromosome names get varied numbers of 'chr' prefixes at various resolutions (i.e. 'chrchrchr1', '1', etc.). Perhaps there are also other bugs resulting in this issue?

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