Skip to content

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

@Saranya-Balachandran

Description

@Saranya-Balachandran

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.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions