Dear RIPSeeker people,

I tried to make RIPSeeker work by testing the system data. But I got an error as below, which seems an error when using biomaRt.

Actually, I checked the host of "dec2011.archive.ensembl.org", which is not down when I run the code.

Here is the code that I used:

 extdata.dir <- system.file("extdata", package="RIPSeeker")

 bamFiles <- list.files(extdata.dir, "\\.bam$", recursive=TRUE, full.names=TRUE)

 bamFiles <- grep("PRC2", bamFiles, value=TRUE)

 # specify control name

 cNAME <- "SRR039214"

 # output file directory

 outDir <- file.path(getwd(), "RIPSeeker_vigenette_example_PRC2")

 # Parameters setting

 binSize <- NULL      # set to NULL to automatically determine bin size

 minBinSize <- 10000  # min bin size in automatic bin size selection

 maxBinSize <- 10100

 multicore <- TRUE

 strandType <- "-"

 biomart <- "ENSEMBL_MART_ENSEMBL"

 biomaRt_dataset <- "mmusculus_gene_ensembl"

 host <- "dec2011.archive.ensembl.org"       

 # host = "www.ensembl.org"

 goAnno <- "org.Mm.eg.db"                  

 seekOut.PRC2 <- ripSeek(bamPath = bamFiles, cNAME = cNAME, reverseComplement = TRUE, genomeBuild = "mm9", strandType = strandType, uniqueHit = TRUE, assignMultihits = TRUE, rerunWithDisambiguatedMultihits = TRUE, binSize=binSize, minBinSize = minBinSize, maxBinSize = maxBinSize, biomart=biomart, host=host, biomaRt_dataset = biomaRt_dataset, goAnno = goAnno, multicore=multicore, outDir=outDir)

........ # the console is truncated from annotation part and the error is as below.

*IV. Annotate RIP regions via online ensembl database (mmusculus_gene_ensembl):

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attributes construct error
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Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'nbsp' not defined
Entity 'raquo' not defined
attributes construct error
Couldn't find end of Start Tag img line 40
Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Entity 'hellip' not defined
Opening and ending tag mismatch: img line 64 and li
Opening and ending tag mismatch: li line 64 and ul
Opening and ending tag mismatch: ul line 63 and div
Entity 'copy' not defined
attributes construct error
Couldn't find end of Start Tag img line 225
attributes construct error
Couldn't find end of Start Tag img line 228
attributes construct error
Couldn't find end of Start Tag img line 231
attributes construct error
Couldn't find end of Start Tag img line 260
Opening and ending tag mismatch: div line 18 and body
Opening and ending tag mismatch: body line 17 and html
Premature end of data in tag html line 2
Error: 1: Entity 'nbsp' not defined
2: attributes construct error
3: Couldn't find end of Start Tag img line 22
4: Entity 'hellip' not defined
5: Entity 'hellip' not defined
6: Entity 'nbsp' not defined
7: Entity 'raquo' not defined
8: attributes construct error
9: Couldn't find end of Start Tag img line 40
10: Entity 'hellip' not defined
11: Entity 'hellip' not defined
12: Entity 'hellip' not defined
13: Entity 'hellip' not defined
14: Entity 'hellip' not defined
15: Opening and ending tag mismatch: img line 64 and li
16: Opening and ending tag mismatch: li line 64 and ul
17: Opening and ending tag mismatch: ul line 63 and div
18: Entity 'copy' not defined
19: attributes construct error
20: Couldn't find end of Start Tag img line 225
21: attributes construct error
22: Couldn't find end of Start Tag img line 228
23: attributes construct error
24: Couldn't find end of Start Tag img line 231
25: attributes construct error
26: Couldn't find end of Start Tag img line 260
27: Opening and e

Hi,

Thanks for reporting the error. Sorry for the late response. Indeed, I'm getting the same error. There seems to be an issue on the Ensembl database query for the archived database.

My package relies on annotatePeakInBatch {ChIPpeakAnno}, which itself relies on useMart {biomaRt}. I got the same error occurs with this:

mart=useMart(biomart='ENSEMBL_MART_ENSEMBL', host="dec2011.archive.ensembl.org")

But querying the latest database seems to work fine (see below). Currently, a quick fix would be to call peaks without annotations and then annotate the peaks using findOverlaps or similar routines by intersecting the peaks (GRanegs) with the gene annotations (downloaded separately from UCSC/Ensembl).

Hope this helps.

Best,

Yue

> x <- annotateRIP(sigGRanges = ripGR, 
+     biomaRt_dataset = dataset, 
+     biomart='ensembl', goAnno="org.Mm.eg.db")

*** Annotating 71 genomic ranges with mmusculus_gene_ensembl.

Loading required package: org.Mm.eg.db
Loading required package: AnnotationDbi

*** GO analysis for 87 associated features with org.Mm.eg.db.

> x
$sigGRangesAnnotated
GRanges object with 87 ranges and 21 metadata columns:
       seqnames                 ranges strand   |    ensembl_gene_id external_gene_name
          <Rle>              <IRanges>  <Rle>   |        <character>        <character>
   [1]     chrX   [ 3893581,  3903615]      -   | ENSMUSG00000101381             Gm3701
   [2]     chrX   [ 7757056,  7777125]      -   | ENSMUSG00000000134               Tfe3
   [3]     chrX   [ 8579926,  8589960]      -   | ENSMUSG00000079701              Ssxb3
   [4]     chrX   [16256701, 16266735]      -   | ENSMUSG00000081312            Gm14520
   [5]     chrX   [20210491, 20220525]      -   | ENSMUSG00000037341             Slc9a7
   ...      ...                    ...    ... ...                ...                ...

Dear Yue,

I guess my error might be cause by the version of genome build that I use. For tophat2 alignment, I used GRCh37 downloaded from genome. But, I found the default recent genome annotation in biomaRt is GRCh38, is't it? If want to use annotation for genome build of hg19, I think I have to change the version. How can I change the annotation version in function of "ripSeek"?

Thanks a lot!

> grch_default = useEnsembl(biomart="ensembl")
> listDatasets(grch_default)[31:35,]
                   dataset                                description      version
31 mlucifugus_gene_ensembl           Myotis lucifugus genes (myoLuc2)      myoLuc2
32   hsapiens_gene_ensembl             Homo sapiens genes (GRCh38.p5)    GRCh38.p5
33   pformosa_gene_ensembl      Poecilia formosa genes (PoeFor_5.1.2) PoeFor_5.1.2
34      mfuro_gene_ensembl Mustela putorius furo genes (MusPutFur1.0) MusPutFur1.0
35 tbelangeri_gene_ensembl           Tupaia belangeri genes (tupBel1)      tupBel1

----------------------------------------

> grch37 = useEnsembl(biomart="ensembl",GRCh=37)
> listDatasets(grch37)[31:35,]
                    dataset                                description      version
31    hsapiens_gene_ensembl            Homo sapiens genes (GRCh37.p13)   GRCh37.p13
32       mfuro_gene_ensembl Mustela putorius furo genes (MusPutFur1.0) MusPutFur1.0
33  tbelangeri_gene_ensembl           Tupaia belangeri genes (tupBel1)      tupBel1
34     ggallus_gene_ensembl              Gallus gallus genes (Galgal4)      Galgal4
35 xtropicalis_gene_ensembl          Xenopus tropicalis genes (JGI4.2)       JGI4.2