Question

diffbind dba.count error "files could not be accessed" on windows 11

1

Entering edit mode

Theo ▴ 10

@theodoregeorgomanolis-7993

Last seen 21 hours ago

Germany

I got the following error while trying to create the initiall dba object:

> tamoxifen <- dba.count(tamoxifen) 
Computing summits...
Error: Some read files could not be accessed. See warnings for details.
In addition: There were 12 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201074_S18_L000/A006200317_201074_S18_L000.bam not accessible
2: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201076_S19_L000/A006200317_201076_S19_L000.bam not accessible
3: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201078_S20_L000/A006200317_201078_S20_L000.bam not accessible
4: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201080_S21_L000/A006200317_201080_S21_L000.bam not accessible
5: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201082_S22_L000/A006200317_201082_S22_L000.bam not accessible
6: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201084_S23_L000/A006200317_201084_S23_L000.bam not accessible
7: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201086_S24_L000/A006200317_201086_S24_L000.bam not accessible
8: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201088_S25_L000/A006200317_201088_S25_L000.bam not accessible
9: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201090_S26_L000/A006200317_201090_S26_L000.bam not accessible
10: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201092_S27_L000/A006200317_201092_S27_L000.bam not accessible
11: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201094_S28_L000/A006200317_201094_S28_L000.bam not accessible
12: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201096_S29_L000/A006200317_201096_S29_L000.bam not accessible

the files are there and using the file.exists I get TRUE at the test. here is a complete code:

read the csv file, I used the sep = \t due to the file being tab delimeted

samples<- read.csv("diffbind.csv",sep = "\t")
> print(samples)
   SampleID   Factor Condition Replicate
1    201074 H3K36me3   control         1
2    201076 H3K36me3   control         2
3    201078 H3K36me3   control         3
4    201080 H3K36me3       AA5         1
5    201082 H3K36me3       AA5         2
6    201084 H3K36me3       AA5         3
7    201086  H4K16ac   control         1
8    201088  H4K16ac   control         2
9    201090  H4K16ac   control         3
10   201092  H4K16ac       AA5         1
11   201094  H4K16ac       AA5         2
12   201096  H4K16ac       AA5         3
                                                                                                                 bamReads
1  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201074_S18_L000/A006200317_201074_S18_L000.bam
2  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201076_S19_L000/A006200317_201076_S19_L000.bam
3  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201078_S20_L000/A006200317_201078_S20_L000.bam
4  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201080_S21_L000/A006200317_201080_S21_L000.bam
5  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201082_S22_L000/A006200317_201082_S22_L000.bam
6  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201084_S23_L000/A006200317_201084_S23_L000.bam
7  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201086_S24_L000/A006200317_201086_S24_L000.bam
8  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201088_S25_L000/A006200317_201088_S25_L000.bam
9  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201090_S26_L000/A006200317_201090_S26_L000.bam
10 Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201092_S27_L000/A006200317_201092_S27_L000.bam
11 Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201094_S28_L000/A006200317_201094_S28_L000.bam
12 Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201096_S29_L000/A006200317_201096_S29_L000.bam
                                                                                                                                                           Peaks
1  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201074_S18_L000/peakcalling/seacr/A006200317_201074_S18_L000_treat.stringent.sort.bed
2  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201076_S19_L000/peakcalling/seacr/A006200317_201076_S19_L000_treat.stringent.sort.bed
3  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201078_S20_L000/peakcalling/seacr/A006200317_201078_S20_L000_treat.stringent.sort.bed
4  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201080_S21_L000/peakcalling/seacr/A006200317_201080_S21_L000_treat.stringent.sort.bed
5  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201082_S22_L000/peakcalling/seacr/A006200317_201082_S22_L000_treat.stringent.sort.bed
6  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201084_S23_L000/peakcalling/seacr/A006200317_201084_S23_L000_treat.stringent.sort.bed
7  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201086_S24_L000/peakcalling/seacr/A006200317_201086_S24_L000_treat.stringent.sort.bed
8  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201088_S25_L000/peakcalling/seacr/A006200317_201088_S25_L000_treat.stringent.sort.bed
9  Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201090_S26_L000/peakcalling/seacr/A006200317_201090_S26_L000_treat.stringent.sort.bed
10 Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201092_S27_L000/peakcalling/seacr/A006200317_201092_S27_L000_treat.stringent.sort.bed
11 Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201094_S28_L000/peakcalling/seacr/A006200317_201094_S28_L000_treat.stringent.sort.bed
12 Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201096_S29_L000/peakcalling/seacr/A006200317_201096_S29_L000_treat.stringent.sort.bed
   PeakCaller scorecol
1         bed        3
2         bed        3
3         bed        3
4         bed        3
5         bed        3
6         bed        3
7         bed        3
8         bed        3
9         bed        3
10        bed        3
11        bed        3
12        bed        3

so the created matrix looks good. lets create the dba object now:

> tamoxifen <- dba(sampleSheet=samples)
201074  H3K36me3 control  1 bed
201076  H3K36me3 control  2 bed
201078  H3K36me3 control  3 bed
201080  H3K36me3 AA5  1 bed
201082  H3K36me3 AA5  2 bed
201084  H3K36me3 AA5  3 bed
201086  H4K16ac control  1 bed
201088  H4K16ac control  2 bed
201090  H4K16ac control  3 bed
201092  H4K16ac AA5  1 bed
201094  H4K16ac AA5  2 bed
201096  H4K16ac AA5  3 bed
> tamoxifen
12 Samples, 3504 sites in matrix (5003 total):
       ID   Factor Condition Replicate Intervals
1  201074 H3K36me3   control         1      3117
2  201076 H3K36me3   control         2      3042
3  201078 H3K36me3   control         3      2888
4  201080 H3K36me3       AA5         1      3245
5  201082 H3K36me3       AA5         2      3014
6  201084 H3K36me3       AA5         3      3278
7  201086  H4K16ac   control         1       114
8  201088  H4K16ac   control         2       117
9  201090  H4K16ac   control         3       171
10 201092  H4K16ac       AA5         1       340
11 201094  H4K16ac       AA5         2       282
12 201096  H4K16ac       AA5         3       249

this also looks good. I am checking if R in windows 11 can actually find the files:

> file.exists(path = samples$bamReads)
 [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
> file.exists(path = samples$Peaks)
 [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE

So all looks ready to do the count

> tamoxifen <- dba.count(tamoxifen) 
Computing summits...
Error: Some read files could not be accessed. See warnings for details.
In addition: There were 12 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201074_S18_L000/A006200317_201074_S18_L000.bam not accessible
2: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201076_S19_L000/A006200317_201076_S19_L000.bam not accessible
3: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201078_S20_L000/A006200317_201078_S20_L000.bam not accessible
4: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201080_S21_L000/A006200317_201080_S21_L000.bam not accessible
5: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201082_S22_L000/A006200317_201082_S22_L000.bam not accessible
6: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201084_S23_L000/A006200317_201084_S23_L000.bam not accessible
7: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201086_S24_L000/A006200317_201086_S24_L000.bam not accessible
8: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201088_S25_L000/A006200317_201088_S25_L000.bam not accessible
9: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201090_S26_L000/A006200317_201090_S26_L000.bam not accessible
10: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201092_S27_L000/A006200317_201092_S27_L000.bam not accessible
11: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201094_S28_L000/A006200317_201094_S28_L000.bam not accessible
12: Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201096_S29_L000/A006200317_201096_S29_L000.bam not accessible

I have no idea how to solve this any clues? SESSION INFO

sessionInfo( )
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale:
[1] LC_COLLATE=English_United Kingdom.utf8  LC_CTYPE=English_United Kingdom.utf8    LC_MONETARY=English_United Kingdom.utf8
[4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.utf8    

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

other attached packages:
 [1] DiffBind_3.8.4              SummarizedExperiment_1.28.0 Biobase_2.58.0              MatrixGenerics_1.10.0      
 [5] matrixStats_0.63.0          GenomicRanges_1.50.2        GenomeInfoDb_1.34.9         IRanges_2.32.0             
 [9] S4Vectors_0.36.2            BiocGenerics_0.44.0        

loaded via a namespace (and not attached):
 [1] bitops_1.0-7             RColorBrewer_1.1-3       numDeriv_2016.8-1.1      tools_4.2.1              utf8_1.2.3              
 [6] R6_2.5.1                 irlba_2.3.5.1            KernSmooth_2.23-20       DBI_1.1.3                colorspace_2.1-0        
[11] apeglm_1.20.0            tidyselect_1.2.0         compiler_4.2.1           cli_3.6.0                DelayedArray_0.24.0     
[16] rtracklayer_1.58.0       caTools_1.18.2           scales_1.2.1             SQUAREM_2021.1           mvtnorm_1.1-3           
[21] mixsqp_0.3-48            stringr_1.5.0            digest_0.6.31            Rsamtools_2.14.0         XVector_0.38.0          
[26] jpeg_0.1-10              pkgconfig_2.0.3          htmltools_0.5.4          fastmap_1.1.1            invgamma_1.1            
[31] bbmle_1.0.25             limma_3.54.2             BSgenome_1.66.3          htmlwidgets_1.6.2        rlang_1.1.0             
[36] rstudioapi_0.14          BiocIO_1.8.0             generics_0.1.3           hwriter_1.3.2.1          BiocParallel_1.32.6     
[41] gtools_3.9.4             dplyr_1.1.2              RCurl_1.98-1.12          magrittr_2.0.3           GenomeInfoDbData_1.2.9  
[46] interp_1.1-4             Matrix_1.5-3             Rcpp_1.0.10              munsell_0.5.0            fansi_1.0.4             
[51] lifecycle_1.0.3          stringi_1.7.12           yaml_2.3.7               MASS_7.3-58.3            zlibbioc_1.44.0         
[56] gplots_3.1.3             plyr_1.8.8               grid_4.2.1               parallel_4.2.1           ggrepel_0.9.3           
[61] bdsmatrix_1.3-6          crayon_1.5.2             deldir_1.0-9             lattice_0.21-8           Biostrings_2.66.0       
[66] locfit_1.5-9.7           pillar_1.9.0             rjson_0.2.21             systemPipeR_2.4.0        codetools_0.2-18        
[71] XML_3.99-0.14            glue_1.6.2               ShortRead_1.56.1         GreyListChIP_1.30.0      latticeExtra_0.6-30     
[76] BiocManager_1.30.20      png_0.1-8                vctrs_0.6.0              gtable_0.3.3             amap_0.8-19             
[81] ashr_2.2-54              ggplot2_3.4.2            emdbook_1.3.12           restfulr_0.0.15          coda_0.19-4             
[86] truncnorm_1.0-9          tibble_3.2.1             GenomicAlignments_1.34.1
>

DiffBind • 847 views

ADD COMMENT • link 9 months ago Theo ▴ 10

score 0 · Answer 1 · 2023-07-13

0

Entering edit mode

James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 16 hours ago

United States

What do you get when you do

file.access(samples$bamReads, 4)

If they are all -1, then you don't have permission to read the files.

ADD COMMENT • link 9 months ago James W. MacDonald 65k

0

Entering edit mode

you hit the spot. But this is a weird issue. Using windows file manager I got, my username as owner. Using WSL2 I am seeing the owner is root and group is again root. permission though are read and write for all. interesting is that I got in the same directory the peaks file that can be accessed without issues, but file.access() gives me a -1. ```R file.access(samples$bamReads, 4) Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201074_S18_L000/A006200317_201074_S18_L000.bam -1

```R
file.access(samples$Peaks, 4)
Z:/Shared folder/Shared data/DNA/NGS_AP01_cfrezza_A006200317/A006200317_201074_S18_L000/peakcalling/seacr/A006200317_201074_S18_L000_treat.stringent.sort.bed

The peak file has been nicely read:

> tamoxifen <- dba(sampleSheet=samples)
201074  H3K36me3 control  1 bed
201076  H3K36me3 control  2 bed
201078  H3K36me3 control  3 bed
201080  H3K36me3 AA5  1 bed
201082  H3K36me3 AA5  2 bed
201084  H3K36me3 AA5  3 bed
201086  H4K16ac control  1 bed
201088  H4K16ac control  2 bed
201090  H4K16ac control  3 bed
201092  H4K16ac AA5  1 bed
201094  H4K16ac AA5  2 bed
201096  H4K16ac AA5  3 bed

class(tamoxifen$peaks)
[1] "list"
summary(tamoxifen$peaks[[1]])
     Chr                Start                End                Score          
 Length:3117        Min.   :    21811   Min.   :    23550   Min.   :0.0004991  
 Class :character   1st Qu.: 34277443   1st Qu.: 34282284   1st Qu.:0.0007487  
 Mode  :character   Median : 75446496   Median : 75451966   Median :0.0007487  
                    Mean   : 75166513   Mean   : 75175177   Mean   :0.0013513  
                    3rd Qu.:110799411   3rd Qu.:110802399   3rd Qu.:0.0009983  
                    Max.   :189858415   Max.   :189866932   Max.   :1.0000000

ADD REPLY • link 9 months ago Theo ▴ 10

0

Entering edit mode

That is weird. No idea why the bed file would be accessible but not the bam. I assume Z: is a samba share? Over the years I have seen people having problems reading files off a samba share on Windows, so maybe it's just something having to do with that. As an example, sometimes people try to put their R library dir on a shared drive and that usually ends in tears. The normal prescription is to tell people not to do that, but moving a bunch of bam files onto your Windows box might not be something you can do.

Sorry I can't be more helpful.

ADD REPLY • link 9 months ago James W. MacDonald 65k

0

Entering edit mode

No worries, moved those locally and that error disaeared. Must to be something woth samba servers. Any way. Now I got another problem and I will open a new question. Thank you James!

ADD REPLY • link 9 months ago Theo ▴ 10