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maxplanck-ie / HiCAssembler

Software to assemble contigs/scaffolds into chromosomes using Hi-C data
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AssertionError #11

Open xinwang-bio opened 5 years ago

xinwang-bio commented 5 years ago

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 "/home/xw/sofware/HiC/bin/assemble", line 308, in main chain_file=args.outFolder + "/liftover.chain") File "/home/xw/sofware/HiC/bin/assemble", line 218, in save_fasta assert(next_contig['start'] - end >= 0) AssertionError

fidelram commented 5 years ago

For some reason the coordinates of a contig are not correct. How are you calling hicassembler?

On Tue, Mar 12, 2019 at 4:25 PM Xin Wang notifications@github.com wrote:

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 "/home/xw/sofware/HiC/bin/assemble", line 308, in main chain_file=args.outFolder + "/liftover.chain") File "/home/xw/sofware/HiC/bin/assemble", line 218, in save_fasta assert(next_contig['start'] - end >= 0) AssertionError

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xinwang-bio commented 5 years ago

@fidelram command is below: assemble -m ctg_10kb_corrected.h5 -o ctg_10kb_corrected_default -f ctg_ident_0.99_cov_0.97_pilon.fasta

ItokawaK commented 4 years ago

I encountered the same issue. I commented out the lines including assert() function, and then the run finished normally. The obtained result looked fine at a glance, but I wonder whether there is any serious problem with this override.

xuxiaoman0212 commented 4 years ago

I got the same error.

Hi fidel, how can I fix it? @fidelram

Thanks for your help.