error: Assertion `c1.pos == c2.mpos' failed

[hzaumsq]

Filling 21 clusters with Hi-C data from SAM file /public/msq/WHF4-1/script//Mi.REduced.paired_only.bam (dot = 1M alignments)
Lachesis: ChromLinkMatrix.cc:2186: void LoadDeNovoCLMsFromSAM(const string&, const string&, const ClusterVec&, std::vector<ChromLinkMatrix*>): Assertion `c1.pos == c2.mpos' failed.

[orange-phoebe]

Hello,
Have you solved this problem? I met the same issue with running LACHESIS. I haven't find out what's wrong with it. How to deal with the error? Could you please provide me any clue about it?
A thousand thanks !

[Lordhooze]

i meet the same problem? any solutions? thank you

[orange-phoebe]

I figured it out with the help of an expert. To solve this problem, you should filter the alignment result with flag >1024 in .SAM file. This Perl script will help:

my ($in, $out) = @argv;
open IN, "$in";
open OUT, ">$out";
while (my $line = ){
if ($line =~ /^@/){
print OUT "$line";
next;
}
my @Flag = split(/\s+/,$line);
next if $flag[1] >= 1024;
print OUT "$line";
}
close IN;

[GitHub-Lujianjun]

Hi，orange-phoebe
Thank you for your suggestions.I don't understand why it could figure out the error after filter flag >1024 in .SAM file.Ok, After filtered, I doubt that the filtered Sam file will affect results?

Looking forward to your kind reply

Lu