HiCAssembler

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Problem with installation

5

Hello, What is the recommenended set up for installation? I have tried to install HiCAssembler in a conda environment with HiCExplorer installed but get this error message: ERROR: Command errored...

MartinLaforest

object of type 'int' has no len() in Scaffolds.py _remove_weakest len(path)

7

One of my former colleague is trying to use HiCAssembler. He launched the following command: ``` assemble -m hic_corrected.h5 -o ./assembly_output --min_scaffold_length 10000 --bin_size 5000 --misassembly_zscore_threshold -1.0 --num_iterations 3 --num_processors...

gtrichard

TypeError: object of type 'int' has no len()

4

Hi When I used this tool, I got an error as below. How can I fix it ? Thanks Hub-hub contact for bin_id:30767 scaffold: tig00000201_arrow_pilon/5_0 degree: 8 with bin_id: 30766...

xinwang-bio

Hello, After correcting the HiC matrix I run into this problem that was already mentioned by other users. I was wondering if you have found a solution. Cheers! WARNING:Scaffolds: Hub-hub...

ManuPoretti

Python 3

5

Hi, I saw that you have the branch 2to3 to migrate HiCAssembler to python 3. As it is getting quite difficult to install all dependencies for python 2.7 I wanted...

dominik-handler

Conflict with Hi-CExplorer

3

I tried to install the HiCAssembler according to the instruction provided by developers, but there is a conflict between the version of hicexplorer (and also cooler) and HiCAssembler. Whereas Hicexplorer...

karimi81

ImportError: No module named HiCMatrix

2

Hi I tried to run HiC Assembler over conda environment with Python 2.7 and an old version of some packages as hicexplorer v2.2 and biopython v1.76 (last supported for Python...

ddelgadillod

Assemble pipeline crashes on iteration 0, "Graph object has no attribute 'node'"

1

Hi there, Could anyone shed some light on any potential issues that might result in 'assemble' crashing with the following error stack: DEBUG:HiCAssembler:iteration: 0 N50: 8,770,000 DEBUG:HiCAssembler:Merging small bins in...

ens-LCampbell

Hi, it happened to me that the pipeline crashes in the last step of outputting the final fasta file with an error like this: ``` DEBUG:HiCAssembler:reordering matrix DEBUG:HiCAssembler:{0: [], 1:...

dominik-handler

Hi author, I tried HiCAssembler, however, there are some errors like: ``` Scaffolds:['ScaffHiC_424/1', 'ScaffHiC_636/2', 'ScaffHiC_424/2', 'ScaffHiC_564'] DEBUG:HiCAssembler:Removing weak edge in path connecting two hic-scaffolds: edge: ('ScaffHiC_636/2', 'ScaffHiC_424/2'), weight: 52731.08417428207 Traceback...

yangxiaofeill