Segmentation fault

[kmnip]

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.

[racon::Polisher::initialize] loaded target sequences
[racon::Polisher::initialize] loaded sequences
[racon::Polisher::initialize] loaded overlaps
[racon::Polisher::initialize] aligned overlap 833/833
[racon::Polisher::initialize] transformed data into windows
[racon::Polisher::polish] generated consensus for window 65/65
Segmentation fault (core dumped)

Here is my command for running Racon:

racon reads.fa reads2targets.paf.gz targets.fa -u > polished_targets.fa

The overlaps were generated with minimap2.

Can you please let me know how I can help you fix this?

Thanks, Ka Ming

[kmnip]

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!

[rvaser]

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

[kmnip]

Hi Robert,

The problematic line has 7522 characters and the CIGAR string has 7315 characters after cg:Z:.

Ka Ming

[cgjosephlee]

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

[kmnip]

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

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