Hello Philippe,
Thanks for sending in this example. Between the time it was originally
reported and your email, Jim Kent fixed the program! We are putting it through
some final testing and will release it with the next set of code changes
(scheduled for Sept 21).
Regards,
----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu
Philippe Veber wrote:
> 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 <http://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] <mailto:[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] <mailto:[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]
> <mailto:[email protected]>> wrote:
> > >
> > >> From: "Jennifer Jackson" <[email protected]
> <mailto:[email protected]>>
> > >> To: [email protected] <mailto:[email protected]>
> > >> Cc: [email protected] <mailto:[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] <mailto:[email protected]> wrote:
> > >>
> > >> > From: [email protected] <mailto:[email protected]>
> > >> > To: [email protected] <mailto:[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]
> <mailto:[email protected]>
> > >> > https://lists.soe.ucsc.edu/mailman/listinfo/genome
> > >> _______________________________________________
> > >> Genome maillist - [email protected]
> <mailto:[email protected]>
> > >> https://lists.soe.ucsc.edu/mailman/listinfo/genome
> > >
> > >
> >
> >
> > _______________________________________________
> > Genome maillist - [email protected]
> <mailto:[email protected]>
> > https://lists.soe.ucsc.edu/mailman/listinfo/genome
> _______________________________________________
> Genome maillist - [email protected]
> <mailto:[email protected]>
> https://lists.soe.ucsc.edu/mailman/listinfo/genome
>
>
_______________________________________________
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