Hello, I am new to DiffBind. I am trying to use dba.count, where ELSDiff is the dba Object after reading the .csv file:

ELSDiff <- dba.count(ELSDiff, bUseSummarizeOverlaps=TRUE)

and I am getting the following Errors:

Indexing Reads/ChipSeqELS5.bam
[E::hts_idx_push] Chromosome blocks not continuous
[E::sam_index] Read 'ChipSeqELS5.10' with ref_name='chr11', ref_length=122082543, flags=0, pos=106583661 cannot be indexed
Indexing Reads/ChipSeqELS6.bam
[E::hts_idx_push] NO_COOR reads not in a single block at the end 0 -1
[E::sam_index] Read 'ChipSeqELS6.54' with ref_name='chr1', ref_length=195471971, flags=0, pos=73532387 cannot be indexed
Indexing Reads/ChipSeqELS7.bam
..........

`

The errors above occur for every .bam file.

I hope you can help. Thank you so much.

Here is a sessionInfo() output:

> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Springdale Open Enterprise Linux 8.4 (Modena)

Matrix products: default
BLAS/LAPACK: /Genomics/argo/users/na1456/miniconda3/envs/narzouni/lib/libopenblasp-r0.3.21.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] DiffBind_3.8.3              SummarizedExperiment_1.28.0
 [3] Biobase_2.58.0              MatrixGenerics_1.10.0      
 [5] matrixStats_0.63.0          GenomicRanges_1.50.2       
 [7] GenomeInfoDb_1.34.4         IRanges_2.32.0             
 [9] S4Vectors_0.36.1            BiocGenerics_0.44.0

Please ignore the post. I think I just figured out what is going on. I am new to DiffBind, so that is why I made this error. The bam files should be sorted.