Question: Error when runing exomePeak
0
gravatar for syrttgump
9 months ago by
syrttgump20
United States
syrttgump20 wrote:

Hi everyone,

I am using exomePeak (v.2.13.2) to call peaks from chip-seq data. This is the command I am using:

result <- exomepeak(GENE_ANNO_GTF=gtf, IP_BAM=f2, INPUT_BAM=f1)

But it fails, the error message is:

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
'select()' returned 1:many mapping between keys and columns
[1] "Divide transcriptome intochr-gene-batch sections ..."
[1] "Get Reads Count ..."
[1] "This step may take a few hours ..."
[1] "100 %"
[1] "Get all the peaks ..."
Error in .subset2(x, i, exact = exact) : subscript out of bounds
Calls: exomepeak ... .report.peak.based.on.result -> [[ -> [[.data.frame -> <Anonymous>
Execution halted

The sessionInfo() output:

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /miniconda/lib/R/lib/libRblas.so
LAPACK: /miniconda/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] exomePeak_2.13.2           GenomicAlignments_1.14.1
 [3] SummarizedExperiment_1.8.0 DelayedArray_0.4.1
 [5] matrixStats_0.53.1         rtracklayer_1.38.3
 [7] GenomicFeatures_1.28.5     AnnotationDbi_1.40.0
 [9] Biobase_2.38.0             Rsamtools_1.30.0
[11] Biostrings_2.46.0          XVector_0.18.0
[13] GenomicRanges_1.30.3       GenomeInfoDb_1.14.0
[15] IRanges_2.12.0             S4Vectors_0.16.0
[17] BiocGenerics_0.24.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17           compiler_3.4.1         prettyunits_1.0.2
 [4] bitops_1.0-6           tools_3.4.1            zlibbioc_1.24.0
 [7] progress_1.2.0         biomaRt_2.34.2         digest_0.6.15
[10] bit_1.1-12             lattice_0.20-34        RSQLite_2.0
[13] memoise_1.1.0          Matrix_1.2-14          DBI_1.0.0
[16] GenomeInfoDbData_1.0.0 stringr_1.3.1          httr_1.3.1
[19] hms_0.3                grid_3.4.1             bit64_0.9-5
[22] R6_2.2.2               XML_3.98-1.11          BiocParallel_1.12.0
[25] blob_1.1.1             magrittr_1.5           assertthat_0.2.0
[28] stringi_1.2.3          RCurl_1.95-4.11        crayon_1.3.4

Here is some lines of my GTF file:

##gff-version 2

##source-version rtracklayer 1.40.3

##date 2018-07-24

NC_007605.1 RefSeq  exon    59  272 .   +   .   transcript_id "gene-HHV4_LMP-2B"; gene_id "gene-HHV4_LMP-2B"; gene_name "LMP-2B"; ID "28"

NC_007605.1 RefSeq  exon    360 458 .   +   .   transcript_id "gene-HHV4_LMP-2B"; gene_id "gene-HHV4_LMP-2B"; gene_name "LMP-2B"; ID "29"

NC_007605.1 RefSeq  exon    540 788 .   +   .   transcript_id "gene-HHV4_LMP-2B"; gene_id "gene-HHV4_LMP-2B"; gene_name "LMP-2B"; ID "30"

NC_007605.1 RefSeq  exon    871 951 .   +   .   transcript_id "gene-HHV4_LMP-2B"; gene_id "gene-HHV4_LMP-2B"; gene_name "LMP-2B"; ID "31"

NC_007605.1 RefSeq  exon    1026    1196    .   +   .   transcript_id "gene-HHV4_LMP-2B"; gene_id "gene-HHV4_LMP-2B"; gene_name "LMP-2B"; ID "32"

NC_007605.1 RefSeq  exon    1280    1495    .   +   .   transcript_id "gene-HHV4_LMP-2B"; gene_id "gene-HHV4_LMP-2B"; gene_name "LMP-2B"; ID "33"

NC_007605.1 RefSeq  exon    1574    1680    .   +   .   transcript_id "gene-HHV4_LMP-2B"; gene_id "gene-HHV4_LMP-2B"; gene_name "LMP-2B"; ID "34"

What is the problem and how can I fix it? Thanks!

 

chipseq exomepeak • 212 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by syrttgump20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 152 users visited in the last hour