Counting reads from BAM files: 'data' must be of a vector type, was 'NULL'

[mbuttner]

Hi,

I ran epiAneufinder on a series of 10X Multiome data and ran into the following issue for 3 out of 8 samples (using the standard cellranger arc output). The other runs were fine.
The crashed runs did not save a count matrix, so there is little I can say about the output. Any suggestions how to fix this?
Thank you!

Subtracting Blacklist...
Adding Nucleotide Information...
1 of 23
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Getting Counts...
Counting reads from bam files .. 
Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x),  : 
  'data' must be of a vector type, was 'NULL'
Calls: epiAneufinder ... as.matrix -> as.matrix -> as.matrix.default -> array
Execution halted

Here's the sessionInfo:

sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS/LAPACK: /home/marenbuettner/miniconda3/envs/apianeufinder/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
 [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
 [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
[10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

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

other attached packages:
 [1] epiAneufinder_0.1.0               cowplot_1.1.1                    
 [3] ggdendro_0.1.23                   ggplot2_3.4.2                    
 [5] magrittr_2.0.3                    BSgenome.Hsapiens.UCSC.hg38_1.4.4
 [7] BSgenome_1.62.0                   rtracklayer_1.54.0               
 [9] plyranges_1.14.0                  data.table_1.14.8                
[11] Matrix_1.5-4                      GenomicAlignments_1.30.0         
[13] Rsamtools_2.10.0                  Biostrings_2.62.0                
[15] XVector_0.34.0                    SummarizedExperiment_1.24.0      
[17] Biobase_2.54.0                    MatrixGenerics_1.6.0             
[19] matrixStats_0.63.0                GenomicRanges_1.46.1             
[21] GenomeInfoDb_1.30.1               IRanges_2.28.0                   
[23] S4Vectors_0.32.4                  BiocGenerics_0.40.0              

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0       lattice_0.21-8         colorspace_2.1-0      
 [4] vctrs_0.6.2            generics_0.1.3         yaml_2.3.7            
 [7] utf8_1.2.3             XML_3.99-0.14          rlang_1.1.1           
[10] R.oo_1.25.0            pillar_1.9.0           glue_1.6.2            
[13] withr_2.5.0            R.utils_2.12.2         BiocParallel_1.28.3   
[16] GenomeInfoDbData_1.2.7 lifecycle_1.0.3        zlibbioc_1.40.0       
[19] munsell_0.5.0          gtable_0.3.3           R.methodsS3_1.8.2     
[22] restfulr_0.0.15        fansi_1.0.4            scales_1.2.1          
[25] DelayedArray_0.20.0    rjson_0.2.21           dplyr_1.1.2           
[28] BiocIO_1.4.0           grid_4.1.3             cli_3.6.1             
[31] tools_4.1.3            bitops_1.0-7           RCurl_1.98-1.12       
[34] tibble_3.2.1           crayon_1.5.2           pkgconfig_2.0.3       
[37] MASS_7.3-58.3          R6_2.5.1               compiler_4.1.3      

[thek71]

Hi Maren,

sorry for the late reply.
We haven't seen this error message before, with the bam based datasets that we used.
Is it possible to send us one of the datasets that causes the error to have a look?
We haven't been able to reproduce your error.

Thank you in advance,
Katia

[mbuttner]

Hi Katia,
thank you for the feedback. Unfortunately, I cannot share the data due to data privacy restrictions. I will revisit the tool and see if I can find a public dataset to reproduce the error.

Best,
Maren

[thek71]

Hi Maren,

one thing that I have noticed in multiome data is that the quality of the reads is not as good as for the scATAC, so it might be that the filtering criteria are high, ending up in empty structures. For the BAM file input we use Rsamtools for the loading and filtering. So far the filtering of the BAM files is mainly hard-coded, but will modify that. In the meantime I would suggest to try and run with the fragments file, just to check that how the quality looks.

Best,
Katia