When I run on a sample individually it runs, but when I add the samplefile it ends in the error listed below.
SessionInfo listed at the very bottom.
Thanks so much,
Tirza Doniger
++++++++++++++++++++
Code:
samples = read.csv("chipQC_samples.csv")
BlackListFile <- "mm10.blacklist.bed"
exampleExp = ChIPQC(samples,annotation="mm10",blacklist = BlackListFile,consensus=TRUE,bcount=FALSE)
Error:
> exampleExp = ChIPQC(samples,annotation="mm10",blacklist = BlackListFile,consensus=TRUE,bcount=FALSE)
4 2 1 macs
6 2 2 macs
19 2 3 macs
20 2 4 macs
29 1 1 macs
32 1 2 macs
33 1 3 macs
37 1 4 macs
Checking chromosomes:
[1] "chr1"
Compiling annotation...
Adding controls...
Computing metrics for 9 samples...
list
Bam file has 22 contigs
Error: BiocParallel errors
element index: 1, 2, 3, 4, 5, 6, ...
first error: could not find function "seqlevels<-"
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=Hebrew_Israel.1255 LC_CTYPE=Hebrew_Israel.1255 LC_MONETARY=Hebrew_Israel.1255 LC_NUMERIC=C
[5] LC_TIME=Hebrew_Israel.1255
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] ChIPQC_1.12.2 DiffBind_2.4.7 ggplot2_2.2.1 DESeq2_1.16.1
[5] SummarizedExperiment_1.6.3 DelayedArray_0.2.7 matrixStats_0.52.2 Biobase_2.36.2
[9] GenomicRanges_1.28.3 GenomeInfoDb_1.12.2 IRanges_2.10.2 S4Vectors_0.14.3
[13] BiocGenerics_0.22.0
loaded via a namespace (and not attached):
[1] amap_0.8-14 colorspace_1.3-2 rjson_0.2.15
[4] hwriter_1.3.2 htmlTable_1.9 XVector_0.16.0
[7] base64enc_0.1-3 ggrepel_0.6.5 bit64_0.9-7
[10] AnnotationDbi_1.38.1 splines_3.4.1 fail_1.3
[13] TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2 geneplotter_1.54.0 knitr_1.16
[16] Formula_1.2-1 Nozzle.R1_1.1-1 Rsamtools_1.28.0
[19] annotate_1.54.0 cluster_2.0.6 GO.db_3.4.1
[22] pheatmap_1.0.8 graph_1.54.0 TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2
[25] compiler_3.4.1 GOstats_2.42.0 backports_1.1.0
[28] assertthat_0.2.0 Matrix_1.2-10 lazyeval_0.2.0
[31] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 limma_3.32.2 acepack_1.4.1
[34] htmltools_0.3.6 tools_3.4.1 bindrcpp_0.2
[37] gtable_0.2.0 glue_1.1.1 GenomeInfoDbData_0.99.0
[40] Category_2.42.1 reshape2_1.4.2 systemPipeR_1.10.0
[43] dplyr_0.7.1 ShortRead_1.34.0 Rcpp_0.12.11
[46] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2 TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2 Biostrings_2.44.1
[49] gdata_2.18.0 rtracklayer_1.36.3 TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0
[52] stringr_1.2.0 gtools_3.5.0 XML_3.98-1.9
[55] edgeR_3.18.1 zlibbioc_1.22.0 scales_0.4.1
[58] RBGL_1.52.0 RColorBrewer_1.1-2 BBmisc_1.11
[61] memoise_1.1.0 gridExtra_2.2.1 biomaRt_2.32.1
[64] rpart_4.1-11 latticeExtra_0.6-28 stringi_1.1.5
[67] RSQLite_2.0 genefilter_1.58.1 checkmate_1.8.3
[70] GenomicFeatures_1.28.4 caTools_1.17.1 BiocParallel_1.10.1
[73] chipseq_1.26.0 rlang_0.1.1 pkgconfig_2.0.1
[76] BatchJobs_1.6 bitops_1.0-6 TxDb.Celegans.UCSC.ce6.ensGene_3.2.2
[79] lattice_0.20-35 bindr_0.1 GenomicAlignments_1.12.1
[82] htmlwidgets_0.8 bit_1.1-12 GSEABase_1.38.0
[85] AnnotationForge_1.18.0 plyr_1.8.4 magrittr_1.5
[88] sendmailR_1.2-1 R6_2.2.2 snow_0.4-2
[91] gplots_3.0.1 Hmisc_4.0-3 DBI_0.7
[94] foreign_0.8-69 survival_2.41-3 RCurl_1.95-4.8
[97] nnet_7.3-12 tibble_1.3.3 KernSmooth_2.23-15
[100] locfit_1.5-9.1 grid_3.4.1 data.table_1.10.4
[103] blob_1.1.0 digest_0.6.12 xtable_1.8-2
[106] brew_1.0-6 munsell_0.4.3
I have the same problem and I'm sure BiocParallel is installed.
Here is my code:
library(ChIPQC)library(BiocParallel)
samples<-read.csv('samples.csv')
ChIPQC(samples)
Here is the output:
WT1 WT 1 macsWT2 WT 2 macs
WT3 WT 3 macs
DKO1 DKO 1 macs
DKO2 DKO 2 macs
DKO3 DKO 3 macs
DosR1 DosR 1 macs
DosR2 DosR 2 macs
DosR3 DosR 3 macs
Checking chromosomes:
[1] "NC_000962.3"
Computing metrics for 9 samples...
list
Bam file has 1 contigs
Error: BiocParallel errors
element index: 1, 2, 3, 4, 5, 6, ...
first error: could not find function "seqlevels<-"
Thank you for your help!
I want to add the Sessioninfo() but the comment can only have 5000 characters. So here is a truncated version of sessioninfo()
R version 3.5.1 (2018-07-02)Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: defaultlocale:[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:[1] parallel stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages:[1] ChIPQC_1.16.0 DiffBind_2.8.0 SummarizedExperiment_1.10.1
[4] DelayedArray_0.6.6 BiocParallel_1.14.2 matrixStats_0.54.0
[7] Biobase_2.40.0 GenomicRanges_1.32.6 GenomeInfoDb_1.16.0
[10] IRanges_2.14.11 S4Vectors_0.18.3 BiocGenerics_0.26.0
[13] ggplot2_3.0.0 BiocInstaller_1.30.0