addGCBias Error in value[[3L]](cond) - truncaded file

[artsvendsen]

Hi,

I'm using chromVAR to analyze bulk ATAC-seq samples where I merge both bam and peakcalled files.
For the FASTA reference I'm using a FaFILE since my samples where aligned to Ensembl 106 release, which is generated with the following lines:

indexFa("~/human/Ensembl_106/Homo_sapiens.GRCh38.dna.primary_assembly.fa")
FaFile.HSapiens.Ensembl.106 <-FaFile("~/human/Ensembl_106/Homo_sapiens.GRCh38.dna.primary_assembly.fa")

(the primary FASTA was downloaded from Ensembl FTP server http://ftp.ensembl.org/pub/release-106/fasta/homo_sapiens/dna/)

When running the analysis with broad peaks, I do not get any issues and the results looks like what we are expecting, however I am now trying to do the same analysis for narrow peaks (same BAM files, same FaFILE, just different MACS2 files), with a small addition of filtering the narrow peaks:

peaks <- readNarrowpeaks(peakfile, width = 500, non_overlapping = TRUE)

but I'm getting an error when running the addGCBias step:

sample_counts <- addGCBias(fragment_counts,
                           genome = FaFile.HSapiens.Ensembl.106)


Error in value[[3L]](cond) :  record 78540 (MT:-33-466) was truncated
  _file: ~/human/Ensembl_106/Homo_sapiens.GRCh38.dna.primary_assembly.fa_

It feels like there might be something wrong with my FASTA file, but since I ran this analysis with broad peaks and it was fine, I assume there's something wrong with the narrow peak analysis, specifically.

I was wondering if you can help me solve this issue. I've attached the narrow peak MACS2 output (there's a .txt at the end so I can properly upload it).

Thanks in advance!

Art.
03_merged_test_full.narrowPeak.txt

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/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    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggrepel_0.9.1        ggplot2_3.3.6        Rsamtools_2.10.0     Biostrings_2.62.0    XVector_0.34.0       GenomicRanges_1.46.1
 [7] GenomeInfoDb_1.30.1  IRanges_2.28.0       S4Vectors_0.32.4     BiocGenerics_0.40.0  BiocParallel_1.28.3  Matrix_1.5-1        
[13] TFBSTools_1.32.0     motifmatchr_1.16.0   chromVAR_1.16.0     

loaded via a namespace (and not attached):
  [1] bitops_1.0-7                matrixStats_0.62.0          DirichletMultinomial_1.36.0 bit64_4.0.5                 httr_1.4.4                 
  [6] tools_4.1.2                 utf8_1.2.2                  R6_2.5.1                    DT_0.25                     KernSmooth_2.23-20         
 [11] lazyeval_0.2.2              seqLogo_1.60.0              DBI_1.1.3                   colorspace_2.0-3            withr_2.5.0                
 [16] tidyselect_1.2.0            bit_4.0.4                   compiler_4.1.2              cli_3.4.1                   Biobase_2.54.0             
 [21] plotly_4.10.0               DelayedArray_0.20.0         labeling_0.4.2              rtracklayer_1.54.0          caTools_1.18.2             
 [26] scales_1.2.1                readr_2.1.3                 stringr_1.4.1               digest_0.6.29               R.utils_2.12.0             
 [31] pkgconfig_2.0.3             htmltools_0.5.3             MatrixGenerics_1.6.0        fastmap_1.1.0               BSgenome_1.62.0            
 [36] htmlwidgets_1.5.4           rlang_1.0.6                 rstudioapi_0.14             RSQLite_2.2.18              shiny_1.7.2                
 [41] farver_2.1.1                BiocIO_1.4.0                generics_0.1.3              jsonlite_1.8.2              vroom_1.6.0                
 [46] gtools_3.9.3                R.oo_1.25.0                 dplyr_1.0.10                RCurl_1.98-1.9              magrittr_2.0.3             
 [51] GO.db_3.14.0                GenomeInfoDbData_1.2.7      Rcpp_1.0.9                  munsell_0.5.0               fansi_1.0.3                
 [56] R.methodsS3_1.8.2           lifecycle_1.0.3             stringi_1.7.8               yaml_2.3.5                  SummarizedExperiment_1.24.0
 [61] zlibbioc_1.40.0             gplots_3.1.3                plyr_1.8.7                  grid_4.1.2                  blob_1.2.3                 
 [66] parallel_4.1.2              promises_1.2.0.1            crayon_1.5.2                miniUI_0.1.1.1              CNEr_1.30.0                
 [71] lattice_0.20-45             annotate_1.72.0             KEGGREST_1.34.0             hms_1.1.2                   pillar_1.8.1               
 [76] rjson_0.2.21                reshape2_1.4.4              TFMPvalue_0.0.8             XML_3.99-0.11               glue_1.6.2                 
 [81] data.table_1.14.2           png_0.1-7                   vctrs_0.4.2                 tzdb_0.3.0                  httpuv_1.6.6               
 [86] tidyr_1.2.1                 purrr_0.3.5                 gtable_0.3.1                poweRlaw_0.70.6             assertthat_0.2.1           
 [91] cachem_1.0.6                mime_0.12                   xtable_1.8-4                restfulr_0.0.15             pracma_2.4.2               
 [96] later_1.3.0                 viridisLite_0.4.1           tibble_3.1.8                GenomicAlignments_1.30.0    AnnotationDbi_1.56.2       
[101] memoise_2.0.1               ellipsis_0.3.2