AssertionError

[xinwang-bio]

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]

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 ***@***.***> 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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#11>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AEu_1fQfa1b9AeqoBBdtfM6Bgjcbld6zks5vV8cBgaJpZM4brKdY> .

[xinwang-bio]

@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]

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]

I got the same error.

Hi fidel, how can I fix it? @fidelram

Thanks for your help.