I have tried running this multiple times. I tried running this with just one BAM file as well to see if it helps with the memory usage. Any tips or help would be appreciated. ```

Specify full path for the BAM file

bam_file <- "C:/Users/amgutierrez/Box/Global transcriptomic analysis human livers/BAM Files/A30.bam.bam"

Specify full paths for reference genome and GTF file

ref_genome <- "C:/Users/amgutierrez/Downloads/GRCh38.primary_assembly.genome.fa.gz" gtf_file <- "C:/Users/amgutierrez/Downloads/gencode.v44.chr_patch_hapl_scaff.annotation.gtf.gz"

Create a transcript database from the GTF file

txdb <- makeTxDbFromGFF(file = gtf_file, format = "gtf")

Build index for the reference genome

buildindex(basename = "ref_genome_index", reference = ref_genome, gappedIndex = FALSE, memory = 4000)

Extract file name without path and extension

bam_file_name <- tools::file_path_sans_ext(basename(bam_file))

Set output BAM file name

output_bam <- paste0(bam_file_name, "_aligned.bam")

Align reads to the reference genome

Rsubread::align(index = "ref_genome_index", input_format = "BAM", readfile1 = bam_file, output_file = output_bam, type = 1) After trying to run this line, the session aborts and says a fatal error occurred

Read the aligned file into an object

alignment <- readGAlignments(out.bam = output_bam)

Check alignment summary

summary(alignment)

sessionInfo() R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 [2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

time zone: America/Los_Angeles tzcode source: internal

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

loaded via a namespace (and not attached): [1] KEGGREST_1.40.0 SummarizedExperiment_1.30.2 [3] rjson_0.2.21 lattice_0.21-8
[5] Biobase_2.60.0 vctrs_0.6.3
[7] tools_4.3.1 bitops_1.0-7
[9] generics_0.1.3 stats4_4.3.1
[11] curl_5.0.1 parallel_4.3.1
[13] tibble_3.2.1 fansi_1.0.4
[15] AnnotationDbi_1.62.2 RSQLite_2.3.1
[17] blob_1.2.4 pkgconfig_2.0.3
[19] Rsubread_2.14.2 Matrix_1.5-4.1
[21] dbplyr_2.3.3 S4Vectors_0.38.1
[23] lifecycle_1.0.3 GenomeInfoDbData_1.2.10
[25] compiler_4.3.1 stringr_1.5.0
[27] Rsamtools_2.16.0 Biostrings_2.68.1
[29] progress_1.2.2 codetools_0.2-19
[31] GenomeInfoDb_1.36.1 RCurl_1.98-1.12
[33] yaml_2.3.7 pillar_1.9.0
[35] crayon_1.5.2 BiocParallel_1.34.2
[37] DelayedArray_0.26.7 cachem_1.0.8
[39] abind_1.4-5 tidyselect_1.2.0
[41] digest_0.6.33 stringi_1.7.12
[43] dplyr_1.1.2 restfulr_0.0.15
[45] grid_4.3.1 biomaRt_2.56.1
[47] fastmap_1.1.1 cli_3.6.1
[49] magrittr_2.0.3 S4Arrays_1.0.5
[51] GenomicFeatures_1.52.1 XML_3.99-0.14
[53] utf8_1.2.3 prettyunits_1.1.1
[55] filelock_1.0.2 rappdirs_0.3.3
[57] bit64_4.0.5 XVector_0.40.0
[59] httr_1.4.6 matrixStats_1.0.0
[61] bit_4.0.5 png_0.1-8
[63] hms_1.1.3 memoise_2.0.1
[65] GenomicRanges_1.52.0 IRanges_2.34.1
[67] BiocIO_1.10.0 BiocFileCache_2.8.0
[69] rtracklayer_1.60.0 rlang_1.1.1
[71] glue_1.6.2 DBI_1.1.3
[73] xml2_1.3.5 BiocGenerics_0.46.0
[75] rstudioapi_0.15.0 R6_2.5.1
[77] MatrixGenerics_1.12.3 GenomicAlignments_1.36.0
[79] zlibbioc_1.46.0