[BioC] GenomicFeatures makeTranscriptDbFromBiomart failure

Thu Jan 5 08:07:59 CET 2012

Hi Tim,

On 11/09/2011 10:27 AM, Hervé Pagès wrote:
> Hi,
>
> On 11-11-09 03:33 AM, Tim Rayner wrote:
>> Hi Marc,
>>
>> Thanks very much for looking into this, and also to Michael for
>> providing the patch. I've upgraded my GRanges package and the code now
>> runs with a couple of warnings:
>>
>>> txdb.Hs2<- makeTranscriptDbFromBiomart(biomart='ensembl',
>>> dataset='hsapiens_gene_ensembl')
>> Download and preprocess the 'transcripts' data frame ... OK
>> Download and preprocess the 'chrominfo' data frame ... FAILED! (=>
>> skipped)
>> Download and preprocess the 'splicings' data frame ... OK
>> Download and preprocess the 'genes' data frame ... OK
>> Prepare the 'metadata' data frame ... OK
>> Make the TranscriptDb object ... OK
>> Warning messages:
>> 1: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels)
>> else paste(labels, :
>> duplicated levels will not be allowed in factors anymore
>> 2: In `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels)
>> else paste(labels, :
>> duplicated levels will not be allowed in factors anymore
>> 3: In .normargChrominfo(chrominfo, transcripts$tx_chrom,
>> splicings$exon_chrom) :
>> chromosome lengths and circularity flags are not available for this
>> TranscriptDb object
>
> The 2 first warnings + the fact that downloading the chrominfo failed
> is not looking good. Didn't use to be like that. We'll investigate on
> our side and report later.

The problem that was preventing makeTranscriptDbFromBiomart() to
fetch the 'chrominfo' data frame (i.e. chromosome lengths) from
Ensembl has been fixed. Make sure you update to the latest version
of GenomicFeatures (v 1.6.5 in BioC release, v 1.7.8 in BioC
devel). Available via biocLite().

The warnings about duplicated levels still need to be investigated.

Cheers,
H.

>
> Cheers,
> H.
>
>>
>> So I think the problem is basically fixed. I wonder if perhaps the
>> issue was caused by truncated data transfers; I observed several
>> similar failures earlier yesterday afternoon, but in each case the
>> problem seemed to occur at a different point in the process.
>>
>> Thanks again,
>>
>> Tim
>>
>> On 8 November 2011 20:16, Marc Carlson<mcarlson at fhcrc.org> wrote:
>>> Hi Tim,
>>>
>>> There was a small bug last week for this method caused by a decision at
>>> ensembl to start supporting psuedoautosomal regions, but it was fixed
>>> last
>>> week and should be fixed with the version of GenomicFeatures reported
>>> here.
>>> I just ran your code locally 4 minutes ago and it still works here. The
>>> only difference I can see is that my GRanges package is one version
>>> higher
>>> than yours (GenomicRanges_1.6.2). Please update that package and then
>>> run
>>> it again and see if you have better luck with ensembl.
>>>
>>> The patch that Michael mentioned actually arrived at the exact moment
>>> that I
>>> was testing the bug fix above which means that it has a some conflicts I
>>> will have to resolve, but it should be added to devel very soon.
>>>
>>>
>>> Marc
>>>
>>>
>>>
>>> On 11/08/2011 03:55 AM, Michael Lawrence wrote:
>>>>
>>>> On Tue, Nov 8, 2011 at 3:19 AM, Tim Rayner<tfrayner at gmail.com> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I'm trying to make a TranscriptDb from the Ensembl human Biomart, but
>>>>> I've run into a problem. As shown below, the equivalent operation for
>>>>> the mouse Biomart works fine:
>>>>>
>>>>>> # Mouse TranscriptDb created without a hitch:
>>>>>> txdb.Mm<- makeTranscriptDbFromBiomart(biomart='ensembl',
>>>>>
>>>>> dataset='mmusculus_gene_ensembl')
>>>>> Download and preprocess the 'transcripts' data frame ... OK
>>>>> Download and preprocess the 'chrominfo' data frame ... OK
>>>>> Download and preprocess the 'splicings' data frame ... OK
>>>>> Download and preprocess the 'genes' data frame ... OK
>>>>> Prepare the 'metadata' data frame ... OK
>>>>> Make the TranscriptDb object ... OK
>>>>>
>>>>>> # Here's the problem:
>>>>>> txdb.Hs<- makeTranscriptDbFromBiomart(biomart='ensembl',
>>>>>
>>>>> dataset='hsapiens_gene_ensembl')
>>>>> Download and preprocess the 'transcripts' data frame ... OK
>>>>> Download and preprocess the 'chrominfo' data frame ... FAILED! (=>
>>>>> skipped)
>>>>> Download and preprocess the 'splicings' data frame ... Error in
>>>>> scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, :
>>>>> line 800380 did not have 11 elements
>>>>>
>>>>>> sessionInfo()
>>>>>
>>>>> R version 2.14.0 (2011-10-31)
>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>>>
>>>>> locale:
>>>>> [1] C
>>>>>
>>>>> attached base packages:
>>>>> [1] stats graphics grDevices utils datasets methods base
>>>>>
>>>>> other attached packages:
>>>>> [1] GenomicFeatures_1.6.1 AnnotationDbi_1.16.0 Biobase_2.14.0
>>>>> [4] GenomicRanges_1.6.1 IRanges_1.12.1
>>>>>
>>>>> loaded via a namespace (and not attached):
>>>>> [1] BSgenome_1.22.0 Biostrings_2.22.0 DBI_0.2-5
>>>>> RCurl_1.6-10
>>>>> [5] RSQLite_0.10.0 XML_3.4-3 biomaRt_2.10.0
>>>>> rtracklayer_1.14.1
>>>>> [9] tools_2.14.0 zlibbioc_1.0.0
>>>>>
>>>>> I don't know if this is an issue with the Biomart instance or the
>>>>> GenomicFeatures package. I was wondering if anyone had any suggestions
>>>>> as to how I might work around this?
>>>>>
>>>>> On a related note, would it be possible to add the ability to point
>>>>> makeTranscriptDbFromBiomart() at alternate Biomart hosts (as one
>>>>> would, for example, by calling
>>>>> biomaRt::useMart(host='www.ensembl.org', ...))?
>>>>
>>>> We've submitted a patch that does just this, as well as supporting an
>>>> attribute prefix string for selecting alternative gene models.
>>>>
>>>>
>>>>> It would probably be
>>>>> good to be able to pass through the 'archive' argument to useMart as
>>>>> well.
>>>>>
>>>>> Many thanks,
>>>>>
>>>>> Tim Rayner
>>>>>
>>>>> --
>>>>> Bioinformatician
>>>>> Smith Lab, CIMR
>>>>> University of Cambridge
>>>>>
>>>>> _______________________________________________
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>>>>>
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>>
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>
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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