Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

HiCLift from cool to hic - invalid literal for int() error #17

Open
Saranya-Balachandran opened this issue Feb 11, 2024 · 0 comments
Open

Comments

@Saranya-Balachandran
Copy link

Dear XiaoTao,
I am trying to convert from cool to hic.
Command used : HiCLift --input hiC/GSE116862_50k_sum.cool --input-format cooler --out-pre GSE116862_sum --output-format hic --in-assembly hg19 --out-assembly hg19 --out-chromsizes hiC/hg19.chrom.sizes

But I encounter the following error:

root INFO @ 02/11/24 21:12:12:

ARGUMENT LIST:

Input path = hiC/GSE116862_50k_sum.cool

Input format = cooler

Output prefix = GSE116862_sum

Output format = hic

Chromosome Sizes of the output assembly = hiC/hg19.chrom.sizes

Generate contact maps at 11 resolutions = False

Input assembly = hg19

Output assembly = hg19

Chain file = None

Temporary Dir = .HiCLift

Allocated memory = 8G

Number of Processes = 8

Log file name = HiCLift.log

root INFO @ 02/11/24 21:12:13: Trying to perform a pure format conversion without liftover ...
HiCLift.utilities INFO @ 02/11/24 21:12:13: Writing headers ...
HiCLift.utilities INFO @ 02/11/24 21:12:13: Dumping contact pairs from hiC/GSE116862_50k_sum.cool ...
Traceback (most recent call last):
File "/work/anaconda3/envs/HiCLift/bin/HiCLift", line 137, in
run()
File "/work/anaconda3/envs/HiCLift/bin/HiCLift", line 110, in run
liftover(
File "/work/anaconda3/envs/HiCLift/lib/python3.9/site-packages/HiCLift/utilities.py", line 178, in liftover
total_count, mapped_count = pixel_to_reads(stdin_wrapper,
File "/work/anaconda3/envs/HiCLift/lib/python3.9/site-packages/HiCLift/io.py", line 190, in pixel_to_reads
s1
, s2
, e1_, e2_, v = int(s1_), int(s2_), int(e1_), int(e2_), int(v)
ValueError: invalid literal for int() with base 10: '212.724'

Thanks for the tool.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant