Hi.
On Fri, May 14, 2010 at 10:36 AM, Markus Leber <leber.mar...@gmx.de> wrote:
> Dear Henrik,
>
> thank you very much for your support.
> You are right. I am sorry that I didn't notice this problem.
> Step "Calibration for crosstalk between allele probe pairs" works without
> problems now.
>
> Unfortunately at the beginning of step "Normalization for nucleotide-position
> probe sequence effects" I noticed another error.
> First I initialize with:
>
> bpn <- BasePositionNormalization(csC, target="zero")
> print(bpn)
>
> Afterwards I call:
>
>> csN <- process(bpn, verbose=verbose)
>
> Within this procedure I noticed this error:
>
> ...
> 20100513 23:03:38| Storing normalized data...
> 20100513 23:03:38| Temporary pathname:
> probeData/HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY/GenomeWideSNP_6/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A03_31250.CEL.tmp
> 20100513 23:03:38| Creating CEL file for results, if missing...
> 20100513 23:03:38| Creating CEL file...
> 20100513 23:03:38| Chip type: GenomeWideSNP_6,Full
> 20100513 23:03:38| Pathname:
> probeData/HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY/GenomeWideSNP_6/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A03_31250.CEL.tmp
> 20100513 23:03:38| Method 'copy'...
> 20100513 23:03:38| Copying file...
> Error in list(`process(bpn, verbose = verbose)` = <environment>,
> `process.AbstractProbeSequenceNormalization(bpn, verbose = verbose)` =
> <environment>, :
>
>
> I printed the workflow & output of this session in file "CRMAv2_Error.txt",
> which is attached.
> Do you have experience with this error or you have an idea about the reason
> of this problem?
It's good that you attach logs, especially when they are really long.
However, there is an advantage of pasting the error message and
traceback into this message, because then it will be found when others
search the archives for similar messages. In your case, if you had
added a little bit more of the error message that would have been
enough for most of us to immediately spot was it going on. From the
end of your CRMAv2_Error.txt log:
20100513 23:03:38| Storing normalized data...
20100513 23:03:38| Temporary pathname:
probeData/HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY/GenomeWideSNP_6/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A03_31250.CEL.tmp
20100513 23:03:38| Creating CEL file for results, if missing...
20100513 23:03:38| Creating CEL file...
20100513 23:03:38| Chip type: GenomeWideSNP_6,Full
20100513 23:03:38| Pathname:
probeData/HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY/GenomeWideSNP_6/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A03_31250.CEL.tmp
20100513 23:03:38| Method 'copy'...
20100513 23:03:38| Copying file...
Fehler in list(`process(bpn, verbose = verbose)` = <environment>,
`process.AbstractProbeSequenceNormalization(bpn, verbose = verbose)` =
<environment>, :
[2010-05-13 23:03:38] Exception: Failed to copy file. Temporary copy
file exists:
probeData/HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY/GenomeWideSNP_6/GIGAS_g_GAINmixHapMapAffy2_GenomeWideEx_6_A03_31250.CEL.tmp.tmp.tmp
at throw(Exception(...))
at throw.default("Failed to copy file. Temporary copy file exists: ", tmpPathn
at throw("Failed to copy file. Temporary copy file exists: ", tmpPathname)
at copyFile.default(getPathname(this), pathname, overwrite = overwrite, verbos
at copyFile(getPathname(this), pathname, overwrite = overwrite, verbose = less
at copyTo.GenericDataFile(this, filename = tmpPathname, path = NULL, verbose =
at copyTo(this, filename = tmpPathname, path = NULL, verbose = less(verbose))
at createFrom.AffymetrixCelFile(df, filename = pathnameT, path = NULL, verbose
at createFrom(df, filename = pathnameT, path = NULL, verbose = less(verbose))
at process.AbstractProbeSequenceNormalization(bpn, verbose = verbose)
at process(bpn, verbose
Zusätzlich: Warnmeldung:
In log2(y) : NaNs wurden erzeugt
20100513 23:03:39| Copying file...done
[...]
See that "traceback"? That is really useful because it tells us what
commands have been called internally and in what function the error
occurs.
EXPLANATION:
The error message tries to be as clear as possible on what the problem
is, even though it does not provide a suggest how to solve (that is
long-term wish I have for the aroma framework). This error thrown in
order to protect you by telling you that there seem to be an existing
temporary file that has been generated but not been completed. It can
either from running the same script simultaneously/in parallel on a
different machine with access to the same file directory, or from a
having interrupted a previous run leaving a half written file. I
suspect the latter is the case for you; did you run it before and the
interrupt it and restarted it?
SOLUTION:
Go to the
probeData/HapMap270,6.0,CEU,testSet,ACC,ra,-XY,BPN,-XY/GenomeWideSNP_6/
directory and delete any files with file extension *.tmp (or
*.tmp.tmp, *.tmp.tmp.tmp and so on). Then restart the script. You
can keep (the two) *.CEL files.
Did it help?
/Henrik
>
> Thank you,
> Markus
> --
> GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT!
> Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
