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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.
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?
The text was updated successfully, but these errors were encountered:
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?
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.quaich/config/config.yml
Lines 2 to 5 in a50deb3
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 fromcooltools/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?
The text was updated successfully, but these errors were encountered: