Hi,
I ran into the very same problem, and I produced a minimal example, see the
files attached.
~/runs 17:18:34 $ ./bedGraphToBigWig failure.bedgraph failure.chrom.sizes
failure.bw
bedGraphToBigWig: bbiWrite.c:346: bbiOutputOneSummaryFurtherReduce:
Assertion `bounds < boundsEnd' failed.
Abandon (core dumped)
By the way, bedGraphToBigWig is not protected against negative coordinates :
if one of the items has a negative ending coordinate, then the following
loop in bedGraphToBigWig.c never ends :
for (resTry = 0; resTry < resTryCount; ++resTry) {
bits32 resEnd = resEnds[resTry];
if (start >= resEnd)
{
resSizes[resTry] += 1;
resEnds[resTry] = resEnd = start + resScales[resTry];
}
while (end > resEnd)
{
resSizes[resTry] += 1;
resEnds[resTry] = resEnd = resEnd + resScales[resTry];
}
}
(about line 170). More precisely the while loop inside never ends.
Hope this helps !
Philippe.
2009/9/9 Ann Zweig <[email protected]>
> Hello Niel,
>
> This error causes concern for us -- sorry you had to encounter it. If
> your data is not proprietary (or behind a firewall), would you consider
> giving me access to it (no need to cc the whole list)? Jim Kent and I would
> then use your data to help troubleshoot the problem with the program.
>
>
> Regards,
>
> ----------
> Ann Zweig
> UCSC Genome Bioinformatics Group
> http://genome.ucsc.edu
>
>
> ----- [email protected] wrote:
>
> > Hi,
> >
> > Yes, I was referring to the linux x86_64 (as far as I can see, that's
> > the
> > only the only program available for bed graph to big wig?)
> >
> > Now I'm getting a new error:
> >
> > bedGraphToBigWig: bbiWrite.c:346: bbiOutputOneSummaryFurtherReduce:
> > Assertion `bounds < boundsEnd' failed.
> > Aborted
> >
> > I really don't think my bedGraph file has positions out of bounds, but
> > I
> > ran it with -clip just in case, and got the same error.
> >
> > Niel
> >
> >
> >
> >
> > > Hi Niel,
> > >
> > > We have also released a cleanly built copy of the linux x86_64
> > > bedGraphToBigWig download, in case that is what you were referring
> > to:
> > >
> > >
> > http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedGraphToBigWig
> > >
> > > Angie
> > >
> > >
> > > ----- "Jennifer Jackson" <[email protected]> wrote:
> > >
> > >> From: "Jennifer Jackson" <[email protected]>
> > >> To: [email protected]
> > >> Cc: [email protected]
> > >> Sent: Friday, September 4, 2009 5:17:17 PM GMT -08:00 US/Canada
> > Pacific
> > >> Subject: Re: [Genome] bedGraphToBigWig
> > >>
> > >> Hello Niel,
> > >>
> > >> Thank you for letting us know about this. Try a fresh build and
> > things
> > >> should work. Plus, here are some new help instructions:
> > >>
> > >> http://genomewiki.ucsc.edu/index.php/Build_Environment_Variables
> > >>
> > >> Please let us know if you continue to have problems,
> > >> Thank you,
> > >> Jennifer
> > >>
> > >> ------------------------------------------------
> > >> Jennifer Jackson
> > >> UCSC Genome Bioinformatics Group
> > >>
> > >> ----- [email protected] wrote:
> > >>
> > >> > From: [email protected]
> > >> > To: [email protected]
> > >> > Sent: Friday, September 4, 2009 12:12:27 PM GMT -08:00 US/Canada
> > >> Pacific
> > >> > Subject: [Genome] bedGraphToBigWig
> > >> >
> > >> > Hi,
> > >> >
> > >> > I'm trying to create a bigWig file out of a bedGraph file. when
> > I
> > >> use
> > >> > the
> > >> > bedGraphToBigWig utility, I get the error:
> > >> >
> > >> > error while loading shared libraries: libssl.so.6: cannot open
> > >> shared
> > >> > object file: No such file or directory
> > >> >
> > >> >
> > >> > I've used bedToBigBed, and get no errors.
> > >> >
> > >> > Any help would be appreciated.
> > >> >
> > >> > Niel
> > >> >
> > >> >
> > >> >
> > >> > _______________________________________________
> > >> > Genome maillist - [email protected]
> > >> > https://lists.soe.ucsc.edu/mailman/listinfo/genome
> > >> _______________________________________________
> > >> Genome maillist - [email protected]
> > >> https://lists.soe.ucsc.edu/mailman/listinfo/genome
> > >
> > >
> >
> >
> > _______________________________________________
> > Genome maillist - [email protected]
> > https://lists.soe.ucsc.edu/mailman/listinfo/genome
> _______________________________________________
> Genome maillist - [email protected]
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
