Recently I am analyzing my CAGE data using CAGEr package and I have experienced some difficulties. My project consists of 10 libraries among which 9 .bam files are up to 940 MB and one .bam is 1.5 GB. At the level of getCTSS(cage_bam) for this one huge file I obtain error:
Reading in file: ./MCF7_xx.bam...
-> Filtering out low quality reads...
Error in .Call2("XStringSet_unlist", x, PACKAGE = "Biostrings") : negative length vectors are not allowed
What I have found is that the issue is caused by size of this huge .bam file. My other .bams work perfectly fine. Moreover, I used SAMtools to extract subset of this huge .bam and it worked perfectly up to size of 1.1 GB. Unfortunately, it is not the solution of my difficulties because .bams are sorted so it cut out part to some extent.
The computing power of my PC is really big, so I guess that the issue is located at different point. In addition, I am using the latest versions of R, RStudio, CAGEr and other adjacent packages @ Ubuntu Unity.
Also, I append sessionInfo():
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS
Matrix products: default
 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=pl_PL.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=pl_PL.UTF-8
 LC_MESSAGES=en_US.UTF-8 LC_PAPER=pl_PL.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=pl_PL.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages:
 BSgenome.Hsapiens.UCSC.hg38_1.4.1 CAGEr_1.18.0 BSgenome_1.44.0 rtracklayer_1.36.3
 Biostrings_2.44.1 XVector_0.16.0 GenomicRanges_1.28.3 GenomeInfoDb_1.12.2
 IRanges_2.10.2 S4Vectors_0.14.3 BiocGenerics_0.22.0
loaded via a namespace (and not attached):
 splines_3.4.1 zlibbioc_1.22.0 GenomicAlignments_1.12.1 beanplot_1.2 BiocParallel_1.10.1
 som_0.3-5.1 lattice_0.20-35 tools_3.4.1 SummarizedExperiment_1.6.3 grid_3.4.1
 data.table_1.10.4 Biobase_2.36.2 matrixStats_0.52.2 Matrix_1.2-10 GenomeInfoDbData_0.99.0
 bitops_1.0-6 RCurl_1.95-4.8 VGAM_1.0-3 DelayedArray_0.2.7 compiler_3.4.1
 Rsamtools_1.28.0 XML_3.98-1.9
I would very appreciate your help how to solve this issue or any suggestions how to skip it.
Thank you in advance and best regards,