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Question: Error When using dba.count() in DiffBind
0
gravatar for ew152
8 months ago by
ew1520
ew1520 wrote:

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? 

ADD COMMENTlink modified 8 months ago by Gord Brown570 • written 8 months ago by ew1520
2
gravatar for Gord Brown
8 months ago by
Gord Brown570
United Kingdom
Gord Brown570 wrote:

Hi,

I've commited a fix to release and devel, so you should see DiffBind 2.6.1 and 2.7.1 as soon as it gets built. 

Sorry for the inconvenience.

 - Gord

ADD COMMENTlink written 8 months ago by Gord Brown570
0
gravatar for Gord Brown
8 months ago by
Gord Brown570
United Kingdom
Gord Brown570 wrote:

Hi,

"croi_count_reads" is a C function for counting.  Most likely your copy of DiffBind is not correctly installed.  Try reinstalling it.  Or use the "bUseSummarizeOverlaps" option to use an alternate counting function.

ADD COMMENTlink written 8 months ago by Gord Brown570

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?

ADD REPLYlink written 8 months ago by ew1520

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!

ADD REPLYlink written 8 months ago by ew1520

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.

ADD REPLYlink written 8 months ago by Gord Brown570

Turns out dba.count *is* broken on R 3.4.2.  I'll get right on that, shall I?

ADD REPLYlink written 8 months ago by Gord Brown570

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!

ADD REPLYlink written 8 months ago by ew1520

I'll post a comment as soon as I check in a fix.
 

ADD REPLYlink written 8 months ago by Gord Brown570

Thank you so much!

ADD REPLYlink modified 8 months ago • written 8 months ago by ew1520
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