Open kmnip opened 5 years ago
I just found out that the segfault has to do with really long CIGAR string in the PAF file. A new PAF file without CIGAR strings has solved the issue for me!
Hi Ka Ming, thanks for reporting this. How long was the CIGAR string? The parser expects the whole line to be shorter than 3000 characters.
Best regards, Robert
Hi Robert,
The problematic line has 7522 characters and the CIGAR string has 7315 characters after cg:Z:
.
Ka Ming
Hi @kmnip ,
I would like to remind that minimap2 use a less precise mapping approach when not outputting cigar string (-c
) in paf format, and may affect racon behavior.
https://github.com/lh3/minimap2/blob/master/FAQ.md#1-alignment-different-with-option--a-or--c
Joseph
Yes, I do see noticable difference in my assembly assessment results. Thanks for the reminder.
On Thu., Aug. 15, 2019, 7:18 p.m. Joseph Lee, notifications@github.com wrote:
Hi @kmnip https://github.com/kmnip ,
I would like to remind that minimap2 use a less precise mapping approach when not outputting cigar string (-c) in paf format, and may affect racon behavior.
https://github.com/lh3/minimap2/blob/master/FAQ.md#1-alignment-different-with-option--a-or--c
Joseph
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/isovic/racon/issues/115?email_source=notifications&email_token=ABJFILW3ZA3XRD2PLM4Y2ELQEYE6LA5CNFSM4HD7ZHGKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4NPHVI#issuecomment-521860053, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJFILVAU7N7CHDVF6TISF3QEYE6LANCNFSM4HD7ZHGA .
Hi,
I am using version 1.3.2 to polish 2 sequences (27903 bp and 4492 bp long) with 835 nanopore reads, but I encountered a segfault after consensus has completed according to the log.
Here is my command for running Racon:
The overlaps were generated with minimap2.
Can you please let me know how I can help you fix this?
Thanks, Ka Ming