Hi Galt and Jennifer,
Thank you so much for your help! I have check my input more carefully and
found that indeed there is one line that has scientific notation. I changed it
and it works now!
Hong
Hong Ji, Ph. D
Postdoc Fellow
Center for Epigenetics
Johns Hopkins School of Medicine
580 Rangos Building,
855 North Wolfe Street
Baltimore, MD 21205
Email:[email protected]
Lab phone: 410-614-3478
----- Original Message -----
From: Galt Barber <[email protected]>
Date: Tuesday, May 18, 2010 4:42 pm
Subject: Re: [Genome] error
To: Jennifer Jackson <[email protected]>
Cc: Hong Ji <[email protected]>, [email protected]
> Hi, Hong!
>
> I just examined the source code to see where
> the error happens and what it means.
>
> The customTrack loader is calling wigEncode.
> wigEncode checks the coordinates of chromStart and chromEnd
> (columns 2 and 3 in many input formats)
> by calling sqlLongLong (or sometimes sqlSigned) in lib/sqlNum.c.
>
> Perhaps the error message would be more specific if it said
> "invalid signed integer" instead of "invalid signed number".
>
> The error message prints out the input exactly as it is,
> i.e. the text itself and not a number or numeric interpretation,
> so it seems very likely that "1.13e+08" does appear in the input.
>
> This sqlLongLong routine reads a piece of ascii text
> and translates it to a long long, or it gives an error.
> It only tolerates an optional leading minus sign [-] and then
> the digits [0-9]. Periods, pluses and the letter e are not allowed.
>
> Can you please check your input wigAscii text again?
>
> Can you send a few lines from the top of your customTrack
> file so I can see exactly what columns of data you have?
>
> Thanks!
>
> FYI from file lib/sqlNum.c:
>
> long long sqlLongLong ( char * s )
> {
> long long res = 0;
> char *p, *p0 = s;
>
> if (*p0 == '-')
> p0++;
> p = p0;
> while ((*p >= '0') && (*p <= '9'))
> {
> res *= 10;
> res += *p - '0';
> p++;
> }
> /* test for invalid character, empty, or just a minus */
> if ((*p != '\0') || (p == p0))
> errAbort("invalid signed number: \"%s\"", s);
> if (*s == '-')
> return -res;
> else
> return res;
> }
>
>
>
> -Galt
>
>
>
> Ar 5/18/2010 12:16 PM, scríobh Jennifer Jackson:
> >Hi Hong,
> >
> >Thanks for the feedback. Good to know the scientific notation is not
> in
> >the data.
> >
> >There are a few things to check:
> >
> >1) Are you loading data through the custom track submission form? The
> >error you sent before looked like a regular "load track" error for users
> >with a mirror. If you want to load as a custom track, with the custom
> >track headers, you must use the custom track submission form.
> >
> >2) There are a few problems with the track line. Clearing these up will
> >likely help.
> >
> >autoScale="off" (remove the "")
> >graphType="bar" (remove the "")
> >
> >
> > (scroll to "Data Values"
> >
> > (see
> >sections THE TYPE FIELD, #14 and OTHER FIELDS).
> >
> >3) Using an alternate data format would likely be much better given the
> >data size. Track line attributes for .wig also work for .bigWig. The
> >".wig" data type is being retired anyway - the recommended replacement
> >is bigWig. See this document for the graphing data types including many
> >links to associated help docs:
> >
> >
> >
> >Conversion program wigToBigWig in the kent source tree or available via
> >ftp pre-compiled here (for some systems):
> >
> >
> >Hopefully this is helpful. Please let us know if you continue to have
> >problems,
> >Jennifer
> >
> >---------------------------------
> >Jennifer Jackson
> >UCSC Genome Informatics Group
> >
> >
> >On 5/18/10 11:44 AM, Hong Ji wrote:
> >>Hi there,
> >> I loaded my track as a custom track and I added the following
> header:
> >>track type=wiggle_0 name="XXX" description="YYY"
> maxHeightPixels=200:100:40 viewLimits=-5.0:5.0 autoScale="off"
> graphType="bar" visibility=full color=250,0,0 altColor=0,100,200 priority=19
> >>
> >>I have check the list and didn't find any scientific notation. I do
> have more than 200,000 rows in my txt file, will that cause any problem?
> >>
> >>Hong
> >>
> >>Hong Ji, Ph. D
> >>Postdoc Fellow
> >>Center for Epigenetics
> >>Johns Hopkins School of Medicine
> >>580 Rangos Building,
> >>855 North Wolfe Street
> >>Baltimore, MD 21205
> >>Email:[email protected]
> >>Lab phone: 410-614-3478
> >>
> >>
> >>
> >>----- Original Message -----
> >>From: Jennifer Jackson<[email protected]>
> >>Date: Monday, May 17, 2010 6:34 pm
> >>Subject: Re: [Genome] error
> >>To: Hong Ji<[email protected]>
> >>Cc: [email protected]
> >>
> >>>Update:
> >>>
> >>>If by chance you are using scientific notation in the input file, that
> >>>may be the root cause of your problems. Try changing those values to
> >>>be fully expanded integers then reload.
> >>>
> >>>As a side note, we will be making the exit more informative when a
> >>>non-integer is expected but not in the input. This will be made
> >>>available in the next code base release at the latest. This change
> >>>will have no impact for actual usage (expanded integers still will
> be
> >>>required), but it should help make the exit less cryptic.
> >>>
> >>>Thank you for letting us know about this and we hope that one of these
> >>>options resolves your loading issues,
> >>>
> >>>Thanks,
> >>>Jennifer
> >>>
> >>>On 5/17/10 3:15 PM, Jennifer Jackson wrote:
> >>>>Hello,
> >>>>
> >>>>The name of your file looks like a custom track, but you are loading
> >>>as
> >>>>a native track into your own mirror? Did you remove all of the
> >>>>browser/track lines from the file before loading?
> >>>>
> >>>>If that is not the problem, please send more details about your exact
> >>>>procedure (assembly, your mirror or genome.ucsc?, load as native track
> >>>>or custom track, small data sample, exact command line arguments -
> if
> >>>>any). We will try to diagnose the problem from there.
> >>>>
> >>>>Thanks,
> >>>>Jennifer
> >>>>
> >>>>---------------------------------
> >>>>Jennifer Jackson
> >>>>UCSC Genome Informatics Group
> >>>>
> >>>>
> >>>>On 5/15/10 9:00 AM, Hong Ji wrote:
> >>>>>I am trying to upload a genome track and keep getting the following
> >>>error:
> >>>>>
> >>>>>track load error (track name='ct_xxx_6191'):
> >>>>>invalid signed number: "1.13e+08"
> >>>>>
> >>>>>I tried to upload the top few lines and it worked. Anyone know
> >>>what’s wrong? Thanks!
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>_______________________________________________
> >>>>>Genome maillist - [email protected]
> >>>>>
> >>>>_______________________________________________
> >>>>Genome maillist - [email protected]
> >>>>
> >_______________________________________________
> >Genome maillist - [email protected]
> >
>
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
