HiCAssembler

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misassembly correction

3

Hi Fidel， I have created a corrected Hi-C matrix in h5 format by HiCExporer，now an assertion error killed the assembly while using the HiCAssembler. " Traceback (most recent call last):...

yongyiyu

AssertionError

4

Hi When I run the HiCAssembler, I got an error like below. How can I fix it ? Traceback (most recent call last): File "/home/xw/sofware/HiC/bin/assemble", line 312, in main(args) File...

xinwang-bio

using HiC-Pro to create maps instead

1

I have used HiC-pro to create maps, is there a way to use this as input to your tool rather than the one you recommend?

rob123king

HiCexplorer version

5

Hi Authors Which HiCexplorer version you used ? I have installed the latest version, But it shows No module named HiCMatrix. Thanks.

xinwang-bio

ValueError: The first argument of bincount must be non-negative

1

Hi Fidel, I am trying to use HiCAssemble to build a genome from Hi-C data. I have analysed the data using HiC-Pro and converted the output to h5 format using...

zhanyinx

Problem with cooler version

4

Hello, When I try to install the program, I encounter the following error : Collecting scandir; python_version < "3.5" (from pathlib2>=2.2.0; python_version < "3.6"->pytest>=2.8.1->HiCAssembler) ERROR: hicmatrix 7 has requirement cooler==0.8.2,...

nadegeguiglielmoni

Assemble self.N50 Error

3

Hi, I'm running `assemble` using this command line: ``` assemble -m hic_corrected.h5 -o ./assembly_output \ --min_scaffold_length 100000 --bin_size 5000 --misassembly_zscore_threshold -1.0 \ --num_iterations 3 --num_processors $THREADS ``` But I'm getting...

francicco

SyntaxError: invalid syntax

1

Hi Fidel, After I installed HiCAssembler, I get this error $assemble Traceback (most recent call last): File "/share/bioinfo/anaconda3/bin/assemble", line 11, in import hicassembler.HiCAssembler as HiCAssembler File "/share/bioinfo/anaconda3/lib/python3.6/site-packages/hicassembler/HiCAssembler.py", line 346 for...

zhuangfjnu