Hello - I'm able to use the ATACseqQC package for handling mouse and human ATACseq data, but have run into an issue specifically with the bamSplit function from this package. This function works just fine with human data, following section 2.4.5 of the vignette here. However, when I pass a .bam file generated from mouse data to this function, I get the following error:

Error in asMethod(object) : 
  cannot create a GRanges object from a Seqinfo object with NA seqlengths

running traceback() shows:

4: stop(wmsg("cannot create a GRanges object ", "from a Seqinfo object with NA seqlengths"))
3: asMethod(object)
2: as(seqinfo(genome)[seqlev], "GRanges")
1: splitBam("myMouseSample.bam", tags = tags, 
       outPath = outPath, txs = txs.ms, genome = genome.ms)

Here's is my code:

library(ATACseqQC)
## input is bamFile
bamfile <- system.file("extdata", "GL1.bam", 
                       package="ATACseqQC", mustWork=TRUE)
## bamfile tags
tags <- c("AS", "XN", "XM", "XO", "XG", "NM", "MD", "YS", "YT")
## files will be output into outPath
outPath <- "splited"
dir.create(outPath)
## shift the bam file by the 5'ends

#using human .bam from above, works fine
library(BSgenome.Hsapiens.UCSC.hg19)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txs.hs <- transcripts(TxDb.Hsapiens.UCSC.hg19.knownGene)
txs.hs <- txs.hs[seqnames(txs.hs) %in% "chr1"]
genome.hs <- Hsapiens
objs <- splitBam(bamfile, tags=tags, outPath=outPath,
                 txs=txs.hs, genome=genome.hs)

#using mouse .bam, produces the error about 'NA seqlengths'
library(BSgenome.Mmusculus.UCSC.mm10)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)
txs.ms <- transcripts(TxDb.Mmusculus.UCSC.mm10.knownGene)
txs.ms <- txs.ms[seqnamestxs.ms) %in% "chr1"]
genome.ms <- Mmusculus
objs <- splitBam("myMouseSample.bam", tags=tags, outPath=outPath,
                 txs=txs.ms, genome=genome.ms)

Session info is:

R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.7 BSgenome.Mmusculus.UCSC.mm10_1.4.0       BSgenome.Hsapiens.UCSC.hg19_1.4.0        BSgenome_1.52.0                         
 [5] rtracklayer_1.44.2                       Biostrings_2.52.0                        XVector_0.24.0                           TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 
 [9] GenomicFeatures_1.36.4                   AnnotationDbi_1.46.0                     Biobase_2.44.0                           GenomicRanges_1.36.0                    
[13] GenomeInfoDb_1.20.0                      IRanges_2.18.1                           ATACseqQC_1.8.5                          S4Vectors_0.22.0                        
[17] BiocGenerics_0.30.0                      edgeR_3.26.5                             biomaRt_2.40.3                           limma_3.40.6                            

loaded via a namespace (and not attached):
  [1] colorspace_1.4-1              seqinr_3.4-5                  grImport2_0.1-5               futile.logger_1.4.3           base64enc_0.1-3               rstudioapi_0.10              
  [7] rGADEM_2.32.0                 ChIPpeakAnno_3.18.2           bit64_0.9-7                   interactiveDisplayBase_1.22.0 splines_3.6.1                 motifStack_1.28.0            
 [13] zeallot_0.1.0                 ade4_1.7-13                   polynom_1.4-0                 Rsamtools_2.0.0               seqLogo_1.50.0                GO.db_3.8.2                  
 [19] dbplyr_1.4.2                  png_0.1-7                     graph_1.62.0                  shiny_1.3.2                   BiocManager_1.30.4            compiler_3.6.1               
 [25] httr_1.4.0                    backports_1.1.4               assertthat_0.2.1              Matrix_1.2-17                 lazyeval_0.2.2                later_0.8.0                  
 [31] formatR_1.7                   htmltools_0.3.6               prettyunits_1.0.2             tools_3.6.1                   gtable_0.3.0                  glue_1.3.1                   
 [37] GenomeInfoDbData_1.2.1        dplyr_0.8.3                   rappdirs_0.3.1                Rcpp_1.0.2                    vctrs_0.2.0                   multtest_2.40.0              
 [43] stringr_1.4.0                 mime_0.7                      ensembldb_2.8.0               XML_3.98-1.20                 idr_1.2                       AnnotationHub_2.16.0         
 [49] zlibbioc_1.30.0               MASS_7.3-51.4                 scales_1.0.0                  hms_0.5.0                     promises_1.0.1                ProtGenerics_1.16.0          
 [55] SummarizedExperiment_1.14.0   RBGL_1.60.0                   AnnotationFilter_1.8.0        lambda.r_1.2.3                yaml_2.2.0                    curl_4.0                     
 [61] memoise_1.1.0                 ggplot2_3.2.0                 MotIV_1.40.0                  stringi_1.4.3                 RSQLite_2.1.2                 randomForest_4.6-14          
 [67] BiocParallel_1.18.0           rlang_0.4.0                   pkgconfig_2.0.2               matrixStats_0.54.0            bitops_1.0-6                  lattice_0.20-38              
 [73] purrr_0.3.2                   GenomicAlignments_1.20.1      htmlwidgets_1.3               bit_1.1-14                    tidyselect_0.2.5              magrittr_1.5                 
 [79] R6_2.4.0                      DelayedArray_0.10.0           DBI_1.0.0                     preseqR_4.0.0                 pillar_1.4.2                  survival_2.44-1.1            
 [85] RCurl_1.95-4.12               tibble_2.1.3                  crayon_1.3.4                  futile.options_1.0.1          KernSmooth_2.23-15            BiocFileCache_1.8.0          
 [91] jpeg_0.1-8                    progress_1.2.2                locfit_1.5-9.1                grid_3.6.1                    blob_1.2.0                    GenomicScores_1.8.1          
 [97] digest_0.6.20                 xtable_1.8-4                  VennDiagram_1.6.20            httpuv_1.5.1                  regioneR_1.16.2               munsell_0.5.0