Hi,
I was trying to use DiffBind to analyze my ATAC-Seq data. When I call the dba.count() function, I got the following error message:
Error: Error processing one or more read files. Check warnings().
In addition: Warning messages:
1: In mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.recursive = TRUE) :
all scheduled cores encountered errors in user code
2: "croi_count_reads" not resolved from current namespace (DiffBind)
3: "croi_count_reads" not resolved from current namespace (DiffBind)
4: "croi_count_reads" not resolved from current namespace (DiffBind)
5: "croi_count_reads" not resolved from current namespace (DiffBind)
6: "croi_count_reads" not resolved from current namespace (DiffBind)
7: "croi_count_reads" not resolved from current namespace (DiffBind)
My sample sheets looks like this:
| SampleID | Tissue | Condition | Replicate | bamReads | Peaks | PeakCaller | PeakFormat |
| S4_colon | Tumor | colon | 2 | /Users/ergangwang/Downloads/Lihua_ATACSeq/rmdupMtUn/CTCTCTAC_S4_L008_R1_001.sorted.rmdupMtUn.bam | /Users/ergangwang/Downloads/Lihua_ATACSeq/macs2/CTCTCTAC_S4_L008_R1_001_peaks.broadPeak | MACS2 | bed |
| S6_colon | Tumor | colon | 3 | /Users/ergangwang/Downloads/Lihua_ATACSeq/rmdupMtUn/CAGAGAGG_S6_L008_R1_001.sorted.rmdupMtUn.bam | /Users/ergangwang/Downloads/Lihua_ATACSeq/macs2/CAGAGAGG_S6_L008_R1_001_peaks.broadPeak | MACS2 | bed |
| S7_colon | Tumor | colon | 4 | /Users/ergangwang/Downloads/Lihua_ATACSeq/rmdupMtUn/LW-L7_S1_L001_R1_001.sorted.rmdupMtUn.bam | /Users/ergangwang/Downloads/Lihua_ATACSeq/macs2/LW-L7_S1_L001_R1_001_peaks.broadPeak | MACS2 | bed |
| S3_liver | Tumor | liver | 2 | /Users/ergangwang/Downloads/Lihua_ATACSeq/rmdupMtUn/GGACTCCT_S3_L008_R1_001.sorted.rmdupMtUn.bam | /Users/ergangwang/Downloads/Lihua_ATACSeq/macs2/GGACTCCT_S3_L008_R1_001_peaks.broadPeak | MACS2 | bed |
| S5_liver | Tumor | liver | 3 | /Users/ergangwang/Downloads/Lihua_ATACSeq/rmdupMtUn/TAGGCATG_S5_L008_R1_001.sorted.rmdupMtUn.bam | /Users/ergangwang/Downloads/Lihua_ATACSeq/macs2/TAGGCATG_S5_L008_R1_001_peaks.broadPeak | MACS2 | bed |
| S8_liver | Tumor | liver | 4 | /Users/ergangwang/Downloads/Lihua_ATACSeq/rmdupMtUn/LW-L8_S2_L001_R1_001.sorted.rmdupMtUn.bam | /Users/ergangwang/Downloads/Lihua_ATACSeq/macs2/LW-L7_S1_L001_R1_001_peaks.broadPeak | MACS2 | bed |
My sessionInfo() looks like this:
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DiffBind_2.6.0 SummarizedExperiment_1.8.0 DelayedArray_0.4.1 matrixStats_0.52.2 Biobase_2.38.0
[6] GenomicRanges_1.30.0 GenomeInfoDb_1.14.0 IRanges_2.12.0 S4Vectors_0.16.0 BiocGenerics_0.24.0
[11] BiocInstaller_1.28.0
loaded via a namespace (and not attached):
[1] Category_2.44.0 bitops_1.0-6 bit64_0.9-7 RColorBrewer_1.1-2 progress_1.1.2
[6] Rgraphviz_2.22.0 tools_3.4.2 backports_1.1.1 R6_2.2.2 KernSmooth_2.23-15
[11] DBI_0.7 lazyeval_0.2.1 colorspace_1.3-2 prettyunits_1.0.2 RMySQL_0.10.13
[16] bit_1.1-12 compiler_3.4.2 sendmailR_1.2-1 graph_1.56.0 rtracklayer_1.38.0
[21] caTools_1.17.1 scales_0.5.0 checkmate_1.8.5 BatchJobs_1.6 genefilter_1.60.0
[26] RBGL_1.54.0 stringr_1.2.0 digest_0.6.12 Rsamtools_1.30.0 AnnotationForge_1.20.0
[31] XVector_0.18.0 base64enc_0.1-3 pkgconfig_2.0.1 limma_3.34.0 rlang_0.1.4
[36] RSQLite_2.0 BBmisc_1.11 bindr_0.1 GOstats_2.44.0 hwriter_1.3.2
[41] BiocParallel_1.12.0 gtools_3.5.0 dplyr_0.7.4 RCurl_1.95-4.8 magrittr_1.5
[46] GO.db_3.5.0 GenomeInfoDbData_0.99.1 Matrix_1.2-11 Rcpp_0.12.13 munsell_0.4.3
[51] stringi_1.1.5 edgeR_3.20.1 zlibbioc_1.24.0 gplots_3.0.1 fail_1.3
[56] plyr_1.8.4 grid_3.4.2 blob_1.1.0 ggrepel_0.7.0 gdata_2.18.0
[61] lattice_0.20-35 Biostrings_2.46.0 splines_3.4.2 GenomicFeatures_1.30.0 annotate_1.56.0
[66] locfit_1.5-9.1 rjson_0.2.15 systemPipeR_1.12.0 biomaRt_2.34.0 glue_1.2.0
[71] XML_3.98-1.9 ShortRead_1.36.0 latticeExtra_0.6-28 gtable_0.2.0 amap_0.8-14
[76] assertthat_0.2.0 ggplot2_2.2.1 xtable_1.8-2 survival_2.41-3 tibble_1.3.4
[81] pheatmap_1.0.8 GenomicAlignments_1.14.0 AnnotationDbi_1.40.0 memoise_1.1.0 bindrcpp_0.2
[86] brew_1.0-6 GSEABase_1.40.0
Could you please tell me what is going wrong here?
Sorry I am new to R. I reinstalled it, and it still gave me the same error. Does it have anything to do with the Mac Clang? Would change my version of R solve this problem?
Hi Gord,
Adding bUseSummarizeOverlaps = TRUE does seems to solve the issue. However, I am just wondering if this would alter the output file or not? Thank you!
Hi,
The output may change a tiny bit. For example, my counting code counts a read if it overlaps a peak by half its length, while summarizeOverlaps may use a slightly different rule (I haven't checked in detail). But I'm confident it won't change the final results noticably.
The version of R and the OS may be part of the problem. I don't have a new enough Mac to test on 10.12, but will check the latest R on 10.10 and let you know if I can reproduce the error.
Turns out
dba.count*is* broken on R 3.4.2. I'll get right on that, shall I?I think dba.count is not working on R 3.4.2, since DiffBind error with dba.count after update this person also posted this problem after they updated their R version (although he said its 3.4.1, but it is posted 7 days ago so I assume he meant 3.4.2). Your help to fix this issue is greatly appreciated, since the different counting algorithm would generate somewhat inconsistency in our results. Please let me know if this issue is solved. Thank you so much Gord!
I'll post a comment as soon as I check in a fix.
Thank you so much!